6RLO

Crystal structure of AT1412dm Fab fragment in complex with CD9 large extracellular loop

• PDB DOI: https://doi.org/10.2210/pdb6RLO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): No 


• Deposited: 2019-05-02 Released: 2021-05-12 
• Deposition Author(s): Neviani, V., Pearce, N.M., Pos, W., Schotte, R., Spits, H., Gros, P.
• Funding Organization(s): Netherlands Organisation for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.287 
• R-Value Work: 0.254 
• R-Value Observed: 0.255 

Starting Model: experimental

Literature

Structural basis of a homo-dimerization site in tetraspanin CD9 targeted by a melanoma patient-derived antibody

Neviani, V., Pos, W., Schotte, R., Wagner, K., Go, D.M., Fatmawati, C., Kedde, M., Claassen, Y.B., Kroon-Batenburg, L., Lutz, M., Verdegaal, E.M.E., van der Burg, S.H., Spits, H., Gros, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 233.99 kDa 
• Atom Count: 15,875 
• Modelled Residue Count: 2,027 
• Deposited Residue Count: 2,132 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AT1412dm Fab Fragment (Heavy Chain)	A, D [auth C], G [auth E], J [auth G]	223	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AT1412dm Fab Fragment (Light Chain)	B, E [auth D], H [auth F], K [auth H]	220	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CD9 antigen	C [auth I], F [auth J], I [auth K], L	90	Homo sapiens	Mutation(s): 0  Gene Names: CD9, MIC3, TSPAN29, GIG2
UniProt & NIH Common Fund Data Resources
Find proteins for P21926 (Homo sapiens) Explore P21926  Go to UniProtKB:  P21926
PHAROS:  P21926 GTEx:  ENSG00000010278

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	P [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	BA [auth F], DA [auth G], EA [auth H], M [auth A], N [auth A], O [auth B], R [auth I], S [auth C], T [auth C], W [auth D], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	AA [auth D], CA [auth F], Q [auth B], U [auth C], V [auth C], Y [auth D], Z [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.287 
• R-Value Work: 0.254 
• R-Value Observed: 0.255 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.776	α = 71.12
b = 89.858	β = 89.59
c = 91.533	γ = 85.96

Software Package:

Software Name	Purpose
DIALS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Neviani, V., Pearce, N.M., Pos, W., Schotte, R., Spits, H., Gros, P.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research	Netherlands	024.002.009

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary