6RLO | pdb_00006rlo

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.287 (Depositor), 0.268 (DCC)
R-Value Work:
0.254 (Depositor)
R-Value Observed:
0.255 (Depositor)

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

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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

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| 3D Structure

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21926
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain DA [auth G] SDF format, chain EA [auth H] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain R [auth I] SDF format, chain T [auth C] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain N [auth A] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth I] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain N [auth A] mmCIF format, chain BA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth I] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain N [auth A]	BA [auth F] DA [auth G] EA [auth H] M [auth A] N [auth A] 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		Interactions Focus chain BA [auth F] Focus chain DA [auth G] Focus chain EA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain R [auth I] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain BA [auth F] Focus chain DA [auth G] Focus chain EA [auth H] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain R [auth I] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain Q [auth B] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain AA [auth D] MOL2 format, chain CA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain AA [auth D] mmCIF format, chain CA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain AA [auth D]	AA [auth D] CA [auth F] Q [auth B] U [auth C] V [auth C] 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		Interactions Focus chain AA [auth D] Focus chain CA [auth F] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth F] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.287 (Depositor), 0.268 (DCC)
R-Value Work: 0.254 (Depositor)
R-Value Observed: 0.255 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

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

Revision History (Full details and data files)

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