7C7I

Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(E30D,K31E)

• PDB DOI: https://doi.org/10.2210/pdb7C7I/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-05-25 Released: 2021-05-05 
• Deposition Author(s): Xiao, L.X., Pan, L.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.246 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 

Literature

Mechanistic Insights into the Interactions of Ras Subfamily GTPases with the SPN Domain of Autism-associated SHANK3.

Xu, X.L., Liu, J.P., Wang, Y.L., Wang, Y., Gong, X., Pan, L.F.

(2020) Chin J Chem 38: 1635-1641

• DOI: https://doi.org/10.1002/cjoc.202000278

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 61.54 kDa 
• Atom Count: 4,304 
• Modelled Residue Count: 509 
• Deposited Residue Count: 532 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rap-1b	A, B	167	Homo sapiens	Mutation(s): 2  Gene Names: RAP1B, OK/SW-cl.11
UniProt & NIH Common Fund Data Resources
Find proteins for P61224 (Homo sapiens) Explore P61224  Go to UniProtKB:  P61224
PHAROS:  P61224 GTEx:  ENSG00000127314

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SH3 and multiple ankyrin repeat domains protein 3	C, D	99	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYB0 (Homo sapiens) Explore Q9BYB0  Go to UniProtKB:  Q9BYB0
PHAROS:  Q9BYB0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP (Subject of Investigation/LOI)	E [auth A], H [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	G [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.246 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.502	α = 90
b = 55.619	β = 90
c = 189.884	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Xiao, L.X., Pan, L.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21822705

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description