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snRNA-activating protein complex subunit 4

Reviewed
Reference proteome

AF-Q5SXM2-F1-v4

DownloadPDB file mmCIF file Predicted aligned error

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Information

Structure viewer
 Very high (pLDDT > 90)
 High (90 > pLDDT > 70)
 Low (70 > pLDDT > 50)
 Very low (pLDDT < 50)
AlphaFold produces a per-residue model confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.

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SequenceNo structure available
Structure Tools
  • 6:37:07
    Mol* Plugin 4.5.0 [8/22/2024, 2:35:37 PM]
 Very high (pLDDT > 90)
 High (90 > pLDDT > 70)
 Low (70 > pLDDT > 50)
 Very low (pLDDT < 50)
AlphaFold produces a per-residue model confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.

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Scored residueAligned residue
02004006008001k1.2k1.4k02004006008001k1.2k1.4k
  • 0
  • 5
  • 10
  • 15
  • 20
  • 25
  • 30
Expected position error (Ångströms)

Predicted aligned error (PAE)

Click and drag a box on the PAE viewer to select regions of the structure and highlight them on the 3D viewer.

PAE data is useful for assessing inter-domain accuracy – go to Help section below for more information.

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114692004006008001,0001,2001,4005001000
2004006008001,0001,2001,400GAVLISTCMDNEQRKHFYWPGAVLISTCMDNEQRKHFYWPAlternative amino acidsResidue sequence number
BenignUncertainPathogenic Reference
Amino acid present in the reference UniProt protein sequence, based on HG38
  • 0.0
  • 0.2
  • 0.3
  • 0.4
  • 0.5
  • 0.6
  • 0.7
  • 0.8
  • 1.0
  • -
Filter by category
0
0.34
0.00.34
0.34
0.56
0.340.564
0.56
1
0.5641
Similar structures Discover similar structures from the Protein Data Bank (PDB) and the AlphaFold Database clustered to 50% sequence identity (AFDB50) using Foldseek.
PDB ID
and chain
DescriptionSpecies Residue
range
E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
Seq.
identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
Res.
(Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
Align
in 3D
Align in 3D
PDB ID and
chain
8ity_4_3
Description

snRNA-activating protein complex subunit 4

snRNA-activating protein co...

snRNA-activating protein complex subunit 4
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1469Q5SXM2

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
3.39e-38
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
100%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.90
Align in 3D
PDB ID and
chain
8iue_4_22
Description

snRNA-activating protein complex subunit 4

snRNA-activating protein co...

snRNA-activating protein complex subunit 4
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1469Q5SXM2

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
3.89e-38
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
100%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
4.10
Align in 3D
PDB ID and
chain
8iuh_4_3
Description

snRNA-activating protein complex subunit 4

snRNA-activating protein co...

snRNA-activating protein complex subunit 4
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1469Q5SXM2

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
1.04e-37
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
100%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.40
Align in 3D
PDB ID and
chain
7xur_A_1
Description

snRNA-activating protein complex subunit 4

snRNA-activating protein co...

snRNA-activating protein complex subunit 4
Species

Homo sapiens

Homo sapiens

Residue range

1 - 505Q5SXM2

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
1.39e-31
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
85.4%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.49
Align in 3D
PDB ID and
chain
7zxe_c_9
Description

snRNA-activating protein complex subunit 4

snRNA-activating protein co...

snRNA-activating protein complex subunit 4
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1469Q5SXM2

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
2.22e-31
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
95.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.50
Align in 3D
PDB ID and
chain
7zwd_c_23
Description

snRNA-activating protein complex subunit 4

snRNA-activating protein co...

snRNA-activating protein complex subunit 4
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1469Q5SXM2

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
3.39e-31
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
95.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.00
Align in 3D
PDB ID and
chain
7zwc_c_7
Description

snRNA-activating protein complex subunit 4

snRNA-activating protein co...

snRNA-activating protein complex subunit 4
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1469Q5SXM2

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
4.48e-31
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
95.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.20
Align in 3D
PDB ID and
chain
7zx7_c_23
Description

snRNA-activating protein complex subunit 4

snRNA-activating protein co...

snRNA-activating protein complex subunit 4
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1469Q5SXM2

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
5.93e-31
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
95.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.40
Align in 3D
PDB ID and
chain
7zx8_c_23
Description

snRNA-activating protein complex subunit 4

snRNA-activating protein co...

snRNA-activating protein complex subunit 4
Species

Homo sapiens

Homo sapiens

Residue range

1 - 1469Q5SXM2

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
7.40e-30
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
95.2%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
3.00
Align in 3D
PDB ID and
chain
1h88_C_2
Description

Transcriptional activator Myb

Transcriptional activator M...

Transcriptional activator Myb
Species

Mus musculus

Mus musculus

Residue range

35 - 193P06876

E-value
Likelihood of a match between
the query and target sequence
in a structural alignment.
The lower the E-value, the more
significant the alignment.
1.17e-7
Seq. identity
Percentage of identical
residues between aligned
sequences over the
aligned length.
33.3%
Resolution (Å)
Resolution. Indicates the level
of detail present in the 3D
structure. Smaller value means
finer details of the structure
and higher quality.
2.80
Items per page:
1 – 10 of 51
AF-Q5SXM2-F1
Current entry

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Aligned in 3D
Rotate and zoom structures in the 3D
viewer. Structures are aligned using alpha
carbon atoms as reference points. Once
aligned, RMSD values will appear in the
list below; lower values indicate greater
similarity between the two structures.
Toggle structures in both PDB and AFDB tables to view and align them with the entry structure in the 3D viewer. You can also download the aligned coordinates of the toggled structures and the entry structure.
Structure similarity clusterPredicted structures in the AlphaFold Protein Structure Database clustered using MMseqs2 and Foldseek. This data is provided by the AFDB Clusters.

AlphaFold database protein sequences clustered by the MMseqs2 algorithm (Steinegger M. and Soeding J., Nat. Commun. 9, 2018). Each cluster is comprised of sequences that fulfil two criteria: maintaining a maximum sequence identity of 50% and achieving a 90% bi-directional sequence overlap with the longest sequence of the cluster representative.

AFDB accession DescriptionSpecies
Sequence length
Average pLDDT
AFDB accessionAF-Q8BP86-F1
Reviewed (Swiss-Prot)
Reference proteome
Description snRNA-activating protein complex subunit 4

snRNA-activating protein complex subunit 4 ...

snRNA-activating protein complex subunit 4
SpeciesMus musculus
Mus musculus
Sequence length 1333 Average pLDDT 53.14
AFDB accessionAF-A0A5S6PR22-F1
Unreviewed
Reference proteome
Description TMC domain-containing protein
TMC domain-containing protein
SpeciesBrugia malayi
Brugia malayi
Sequence length 1518 Average pLDDT 52.46
AFDB accessionAF-A0A212CX01-F1
Unreviewed
Reference proteome
Description Uncharacterized protein
Uncharacterized protein
SpeciesCervus elaphus hippelaphus
Cervus elaphus hippelaphus
Sequence length 1221 Average pLDDT 49.72
AFDB accessionAF-A0A6J0DIZ8-F1
Unreviewed
Reference proteome
Description snRNA-activating protein complex subunit 4 isoform X2

snRNA-activating protein complex subunit 4 isoform X2 ...

snRNA-activating protein complex subunit 4 isoform X2
SpeciesPeromyscus maniculatus bairdii
Peromyscus maniculatus bairdii
Sequence length 1264 Average pLDDT 48.03
AFDB accessionAF-A0A3L7HF24-F1
Unreviewed
Reference proteome
Description SNAPC4
SNAPC4
SpeciesCricetulus griseus
Cricetulus griseus
Sequence length 1229 Average pLDDT 47.97
AFDB accessionAF-A0A0L7M148-F1
Unreviewed
Reference proteome
Description Uncharacterized protein
Uncharacterized protein
SpeciesPlasmodium falciparum (isolate Dd2)
Plasmodium falciparum (isolate Dd2)
Sequence length 1209 Average pLDDT 35.78
Items per page:
1 – 6 of 6

Help

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How to interpret the Predicted Aligned Error

 

The Predicted Aligned Error (PAE) measures the confidence in the relative position of two residues within the predicted structure, providing insight into the reliability of relative position and orientations of different domains. Consider the human protein encoded by the gene GNE (Q9Y223).

GNE has two distinct domains according to experimentally determined structures in the Protein Data Bank (PDBe-KB). Does AlphaFold confidently predict their relative positions? We can use the interactive Predicted Aligned Error (PAE) plot to answer this question.

The PAE plot is not an inter-residue distance map or a contact map. Instead, the shade of green indicates the expected distance error in Ångströms (Å), ranging from 0 Å to an arbitrary cut-off of 31 Å. The colour at (x, y) corresponds to the expected distance error in the residue x’s position when the predicted and the true structures are aligned on residue y.

A dark green tile corresponds to a good prediction (low error), whereas a light green tile indicates poor prediction (high error). For example, when aligning on residue 300:

  • We’re confident in the relative position of residue 200
  • We’re not confident in the relative position of residue 600

The two low-error, dark green squares correspond to the two domains. By clicking and dragging, you can highlight these squares on the structure. If you want to remove the highlighting, click the cross icon.

When selecting an off-diagonal region, the plot visually represents the relationship between the selected ranges on the sequence and structure. The x range corresponds to the selection for scored residues, highlighted in orange, while the y range of aligned residues is highlighted in emerald green.

The high PAE values across the whole inter-domain region indicate that for this particular protein, AlphaFold does not reliably predict the relative position of the domains.

Let’s consider another inter-domain example, the human protein encoded by DIP2B (Q9P265).

In this case, we have confidence in the relative position of scored residues around 1450 when aligned with residues around 850, suggesting a packing between the small central domains.

Note that the PAE scores are asymmetrical, meaning there might be variations in PAE values between (x,y) and (y,x) positions. This is particularly relevant for loop regions with highly uncertain orientations, as seen on the DNA topoisomerase 3 (Q8T2T7).

 


Last updated

Last updated in AlphaFold DB version 2022-11-01, created with the AlphaFold Monomer v2.0 pipeline.

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If you make use of an AlphaFold prediction, please cite the following papers:
Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021).
Varadi, M et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Research (2024).
If you use data from AlphaMissense in your work, please cite the following paper:
Cheng, J et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science (2023).

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AlphaMissense Copyright (2023) DeepMind Technologies Limited.

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