6TA7 | pdb_00006ta7

CRYSTAL STRUCTURE OF HUMAN G3BP1-NTF2 IN COMPLEX WITH HUMAN CAPRIN1-DERIVED SOLOMON MOTIF

PDB DOI: https://doi.org/10.2210/pdb6TA7/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-10-29 Released: 2021-05-12
Deposition Author(s): Schulte, T., Achour, A., Panas, M.D., McInerney, G.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.252 (Depositor), 0.258 (DCC)
R-Value Work:
0.207 (Depositor), 0.215 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Caprin-1 binding to the critical stress granule protein G3BP1 is regulated by pH

Schulte, T., Panas, M.D., Williams, L., Kedersha, N., Fleck, J.S., Tan, T.J., Olsson, A., Morro, A.M., Hanke, L., Nilvebrant, J., Giang, K.A., Nygren, P.A., Anderson, P., Achour, A., McInerney, G.M.

(2021) bioRxiv

DOI: https://doi.org/10.1101/2021.02.05.429362

Macromolecule Content

Total Structure Weight: 103.47 kDa
Atom Count: 6,516
Modeled Residue Count: 792
Deposited Residue Count: 902
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras GTPase-activating protein-binding protein 1	A B C [auth D] D [auth F] G [auth C] A, B, C [auth D], D [auth F], G [auth C], H [auth E]	140	Homo sapiens	Mutation(s): 0 Gene Names: G3BP1, G3BP EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13283 (Homo sapiens) Explore Q13283 Go to UniProtKB: Q13283
PHAROS: Q13283 GTEx: ENSG00000145907
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13283
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caprin-1	E [auth G], F [auth H]	31	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q14444 (Homo sapiens) Explore Q14444 Go to UniProtKB: Q14444
PHAROS: Q14444 GTEx: ENSG00000135387
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14444
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth D]	I [auth A], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.252 (Depositor), 0.258 (DCC)
R-Value Work: 0.207 (Depositor), 0.215 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.558	α = 90
b = 100.038	β = 90
c = 113.345	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
Coot	model building
MxCuBE	data collection
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

McInerney, G.M.

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.