6RLM

Crystal structure of AT1412dm Fab fragment

• PDB DOI: https://doi.org/10.2210/pdb6RLM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• 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: 2.50 Å
• R-Value Free: 0.267 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 

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 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 6 assigned by authors and generated by PISA (software)

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 7 assigned by authors and generated by PISA (software)

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 8 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 388.5 kDa 
• Atom Count: 26,544 
• Modelled Residue Count: 3,466 
• Deposited Residue Count: 3,576 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AT1412dm Fab (Heavy Chain)	A, C, E, G, I, K, M, O	227	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AT1412dm Fab (Light Chain)	B, D, F, H, J, L, N, P	220	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	Q [auth C], R [auth G], S [auth J], T [auth K]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.267 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.909	α = 90
b = 238.594	β = 90
c = 209.812	γ = 90

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: 2024-10-16
  Changes: Structure summary