3MNV | pdb_00003mnv

Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment

PDB DOI: https://doi.org/10.2210/pdb3MNV/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2010-04-22 Released: 2010-11-17
Deposition Author(s): Nicely, N.I., Dennison, S.M., Kelsoe, G., Liao, H.-X., Alam, S.M., Haynes, B.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.228 (Depositor), 0.216 (DCC)
R-Value Work:
0.181 (Depositor), 0.169 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a non-neutralizing antibody to the HIV-1 gp41 membrane-proximal external region.

Nicely, N.I., Dennison, S.M., Spicer, L., Scearce, R.M., Kelsoe, G., Ueda, Y., Chen, H., Liao, H.X., Alam, S.M., Haynes, B.F.

(2010) Nat Struct Mol Biol 17: 1492-1494

PubMed: 21076400 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.1944
Primary Citation Related Structures:
3MNV

PubMed Abstract:
The monoclonal antibody 13H11 shares part of its epitope in the HIV-1 gp41 membrane-proximal external region (MPER) with the rare, broadly neutralizing human antibody 2F5. Although 13H11 partially cross-blocked 2F5 binding, 13H11 is non-neutralizing and does not block 2F5 neutralization. We show that unlike 2F5, 13H11 binds to a well-defined helical MPER structure that is consistent with the structure of gp41 in a post-fusion six-helix bundle conformation.

Organizational Affiliation

Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA. nathan.nicely@duke.edu

Macromolecule Content

Total Structure Weight: 97.4 kDa
Atom Count: 7,087
Modeled Residue Count: 857
Deposited Residue Count: 886
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN	A, C	224	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for Q8TCD0 (Homo sapiens) Explore Q8TCD0 Go to UniProtKB: Q8TCD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TCD0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN	B, D	219	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for Q6N089 (Homo sapiens) Explore Q6N089 Go to UniProtKB: Q6N089
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N089
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A] F [auth B] G [auth B] H [auth B] M [auth C] E [auth A], F [auth B], G [auth B], H [auth B], M [auth C], N [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain M [auth C] Focus chain N [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B], K [auth B], O [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.228 (Depositor), 0.216 (DCC)
R-Value Work: 0.181 (Depositor), 0.169 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.378	α = 90
b = 158.378	β = 90
c = 92.975	γ = 120

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-11-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-11-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-08-16
Changes: Source and taxonomy
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-27
Changes: Structure summary