5ZMJ | pdb_00005zmj

Crystal structure of the Fab region of a neutralizing fully human antibody against GM-CSF

PDB DOI: https://doi.org/10.2210/pdb5ZMJ/pdb

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

Deposited: 2018-04-04 Released: 2019-04-17
Deposition Author(s): Angkawidjaja, C., Torashima, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.191 (Depositor), 0.213 (DCC)
R-Value Work:
0.161 (Depositor)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the Fab region of a neutralizing antibody against granulocyte-macrophage colony-stimulating factor.

Angkawidjaja, C., Torashima, T.

(2019) Acta Crystallogr F Struct Biol Commun 75: 634-639

PubMed: 31584011 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X1901238X
Primary Citation Related Structures:
5ZMJ

PubMed Abstract:
An increased level of granulocyte-macrophage colony-stimulating factor has a potential role in the development of autoimmune diseases, and the neutralization of its activity by monoclonal antibodies is a promising therapy for some diseases. Here, the crystal structure of the Fab region of EV1007, a fully human antibody expressed in Chinese hamster ovary cells that was developed from human peripheral blood mononuclear cells, is described. The structure closely resembles that of MB007, which is the Fab region of the same antibody expressed in Escherichia coli [Blech et al. (2012), Biochem. J. 447, 205-215], except at the hinge regions between the immunoglobulin domains and the H3 loop region. This paper presents evidence for the flexibility of the hinge and H3 loop regions of the antibody based on the comparison of two independently solved crystal structures.

Organizational Affiliation

Antibody Drug Discovery Laboratory, Evec Inc., Technopark 1-chome, Sapporo Electronics Center, Sapporo, Hokkaido, Japan.

Macromolecule Content

Total Structure Weight: 52.37 kDa
Atom Count: 3,830
Modeled Residue Count: 438
Deposited Residue Count: 483
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of a Fab fraction of human IgG	A [auth H]	248	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of a Fab fraction of human IgG	B [auth L]	235	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth L] SDF format, chain I [auth L] SDF format, chain H [auth L] SDF format, chain G [auth L] SDF format, chain F [auth L] SDF format, chain C [auth H] MOL2 format, chain J [auth L] MOL2 format, chain I [auth L] MOL2 format, chain H [auth L] MOL2 format, chain G [auth L] MOL2 format, chain F [auth L] MOL2 format, chain C [auth H] mmCIF format, chain J [auth L] mmCIF format, chain I [auth L] mmCIF format, chain H [auth L] mmCIF format, chain G [auth L] mmCIF format, chain F [auth L] mmCIF format, chain C [auth H]	C [auth H] F [auth L] G [auth L] H [auth L] I [auth L] C [auth H], F [auth L], G [auth L], H [auth L], I [auth L], J [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth H] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Interactions & Density Focus chain C [auth H] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L SDF format, chain K [auth L] SDF format, chain E [auth H] SDF format, chain D [auth H] MOL2 format, chain L MOL2 format, chain K [auth L] MOL2 format, chain E [auth H] MOL2 format, chain D [auth H] mmCIF format, chain L mmCIF format, chain K [auth L] mmCIF format, chain E [auth H] mmCIF format, chain D [auth H]	D [auth H], E [auth H], K [auth L], L	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain E [auth H] Focus chain K [auth L] Focus chain L Interactions & Density Focus chain D [auth H] Focus chain E [auth H] Focus chain K [auth L] Focus chain L

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.191 (Depositor), 0.213 (DCC)
R-Value Work: 0.161 (Depositor)
R-Value Observed: 0.163 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.12	α = 90
b = 66.69	β = 90
c = 129.04	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
pointless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-04-17

Deposition Author(s):

Angkawidjaja, C.

Torashima, T.

Revision History (Full details and data files)

Version 1.0: 2019-04-17
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary