5JHG | pdb_00005jhg

Crystal structure of the complex between the human RhoA and the DH/PH domain of human ARHGEF11

PDB DOI: https://doi.org/10.2210/pdb5JHG/pdb

Classification: SIGNALING PROTEIN/TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-04-21 Released: 2017-04-26
Deposition Author(s): Wang, R., Chen, Q., Zhang, H., Yan, Z., Li, J., Miao, L., Wang, F.
Funding Organization(s): Jiangsu Province science and technology plan items (Jiangsu Province science and technology enterprise technology innovation Fund)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.270 (Depositor), 0.269 (DCC)
R-Value Work:
0.221 (Depositor), 0.222 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5JHG

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

Literature

Crystallization and preliminary X-ray crystallographic analysis of a small GTPase RhoA bound with its inhibitor and ARHGEF11

Wang, R., Yan, Z., Lv, Z., Ma, L., Wang, F., Li, J., Miao, L.

To be published.

Macromolecule Content

Total Structure Weight: 127.12 kDa
Atom Count: 8,796
Modeled Residue Count: 1,070
Deposited Residue Count: 1,100
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho guanine nucleotide exchange factor 11	A, C [auth E]	369	Homo sapiens	Mutation(s): 0 Gene Names: ARHGEF11, KIAA0380
UniProt & NIH Common Fund Data Resources
Find proteins for O15085 (Homo sapiens) Explore O15085 Go to UniProtKB: O15085
PHAROS: O15085 GTEx: ENSG00000132694
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15085
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein RhoA	B, D [auth F]	181	Homo sapiens	Mutation(s): 0 Gene Names: RHOA, ARH12, ARHA, RHO12 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61586 (Homo sapiens) Explore P61586 Go to UniProtKB: P61586
PHAROS: P61586 GTEx: ENSG00000067560
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61586
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth E] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth E] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth E]	E [auth A], F [auth A], G [auth B], H [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth E] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.270 (Depositor), 0.269 (DCC)
R-Value Work: 0.221 (Depositor), 0.222 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.44	α = 90
b = 118.589	β = 113
c = 88.003	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-04-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Jiangsu Province science and technology plan items (Jiangsu Province science and technology enterprise technology innovation Fund)	China	BC2013062

Revision History (Full details and data files)

Version 1.0: 2017-04-26
Type: Initial release
Version 1.1: 2024-03-20
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.