8BNT | pdb_00008bnt

The DH domain of ARHGEF2 bound to RhoA

PDB DOI: https://doi.org/10.2210/pdb8BNT/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-11-25 Released: 2022-12-07
Deposition Author(s): Bradshaw, W.J., Katis, V.L., Grosjean, H., Bountra, C., von Delft, F., Brennan, P.E.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.175 (Depositor), 0.174 (DCC)
R-Value Work:
0.130 (Depositor), 0.130 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The DH domain of ARHGEF2 bound to RhoA

Bradshaw, W.J., Katis, V.L., Grosjean, H., Bountra, C., von Delft, F., Brennan, P.E.

To be published.

Macromolecule Content

Total Structure Weight: 50.65 kDa
Atom Count: 4,183
Modeled Residue Count: 424
Deposited Residue Count: 430
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein RhoA	A	185	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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho guanine nucleotide exchange factor 2	B	245	Homo sapiens	Mutation(s): 0 Gene Names: ARHGEF2, KIAA0651, LFP40
UniProt & NIH Common Fund Data Resources
Find proteins for Q92974 (Homo sapiens) Explore Q92974 Go to UniProtKB: Q92974
PHAROS: Q92974 GTEx: ENSG00000116584
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92974
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.175 (Depositor), 0.174 (DCC)
R-Value Work: 0.130 (Depositor), 0.130 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.432	α = 90
b = 71.432	β = 90
c = 196.527	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	5U54AG065187-03

Revision History (Full details and data files)

Version 1.0: 2022-12-07
Type: Initial release
Version 1.1: 2023-05-03
Changes: Database references, Source and taxonomy, Structure summary
Version 1.2: 2024-02-07
Changes: Data collection, Refinement description