3GBM | pdb_00003gbm

Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin.

PDB DOI: https://doi.org/10.2210/pdb3GBM/pdb

Classification: viral protein / immune system
Organism(s): Influenza A virus (A/Viet Nam/1203/2004(H5N1)), Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2009-02-20 Released: 2009-03-10
Deposition Author(s): Ekiert, D.C., Elsliger, M.A., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.261 (Depositor), 0.272 (DCC)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.206 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Antibody recognition of a highly conserved influenza virus epitope.

Ekiert, D.C., Bhabha, G., Elsliger, M.A., Friesen, R.H., Jongeneelen, M., Throsby, M., Goudsmit, J., Wilson, I.A.

(2009) Science 324: 246-251

PubMed: 19251591 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1171491
Primary Citation Related Structures:
3GBM, 3GBN

PubMed Abstract:
Influenza virus presents an important and persistent threat to public health worldwide, and current vaccines provide immunity to viral isolates similar to the vaccine strain. High-affinity antibodies against a conserved epitope could provide immunity to the diverse influenza subtypes and protection against future pandemic viruses. Cocrystal structures were determined at 2.2 and 2.7 angstrom resolutions for broadly neutralizing human antibody CR6261 Fab in complexes with the major surface antigen (hemagglutinin, HA) from viruses responsible for the 1918 H1N1 influenza pandemic and a recent lethal case of H5N1 avian influenza. In contrast to other structurally characterized influenza antibodies, CR6261 recognizes a highly conserved helical region in the membrane-proximal stem of HA1 and HA2. The antibody neutralizes the virus by blocking conformational rearrangements associated with membrane fusion. The CR6261 epitope identified here should accelerate the design and implementation of improved vaccines that can elicit CR6261-like antibodies, as well as antibody-based therapies for the treatment of influenza.

Organizational Affiliation

Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 213.73 kDa
Atom Count: 14,189
Modeled Residue Count: 1,829
Deposited Residue Count: 1,916
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C	334	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0 Gene Names: HA, Hemagglutinin (HA)
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33 Go to UniProtKB: Q6DQ33
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DQ33
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain C
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D	177	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0 Gene Names: HA, Hemagglutinin (HA)
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33 Go to UniProtKB: Q6DQ33
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DQ33
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody (Fab)	E [auth H], G [auth I]	226	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody (Fab)	F [auth L], H [auth M]	221	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth E], J [auth F]	2		N-Glycosylation	Interactions Focus chain I [auth E] Focus chain J [auth F] Interactions & Density Focus chain I [auth E] Focus chain J [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D]	K [auth A], M [auth A], O [auth B], R [auth C], T [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain T [auth D] Interactions & Density Focus chain K [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain T [auth D]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth C] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth C]	L [auth A], Q [auth C]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain L [auth A] Focus chain Q [auth C] Interactions & Density Focus chain L [auth A] Focus chain Q [auth C]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain S [auth C] MOL2 format, chain N [auth A] MOL2 format, chain S [auth C] mmCIF format, chain N [auth A] mmCIF format, chain S [auth C]	N [auth A], S [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain S [auth C] Interactions & Density Focus chain N [auth A] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.261 (Depositor), 0.272 (DCC)
R-Value Work: 0.203 (Depositor)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 202.761	α = 90
b = 202.761	β = 90
c = 202.761	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-03-10

Deposition Author(s):

Ekiert, D.C.

Elsliger, M.A.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2009-03-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary