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- PDB-8gpk: Crystal structure of human anti-HIV-1 broadly neutralizing antibo... -

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Basic information

Entry
Database: PDB / ID: 8gpk
TitleCrystal structure of human anti-HIV-1 broadly neutralizing antibody F6 Fab
Components
  • F6 Fab heavy Chain
  • F6 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / HIV-1 / Env binding
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsNiu, J. / Yang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Structures and immune recognition of Env trimers from two Asia prevalent HIV-1 CRFs.
Authors: Jun Niu / Qi Wang / Wenwen Zhao / Bing Meng / Youwei Xu / Xianfang Zhang / Yi Feng / Qilian Qi / Yanling Hao / Xuan Zhang / Ying Liu / Jiangchao Xiang / Yiming Shao / Bei Yang /
Abstract: Structure-guided immunofocusing HIV-1 vaccine design entails a comprehensive understanding of Envs from diverse HIV-1 subtypes, including circulating recombinant forms (CRFs). Here, we present the ...Structure-guided immunofocusing HIV-1 vaccine design entails a comprehensive understanding of Envs from diverse HIV-1 subtypes, including circulating recombinant forms (CRFs). Here, we present the cryo-EM structures of Envs from two Asia prevalent CRFs (CRF01_AE and CRF07_BC) at 3.0 and 3.5 Å. We compare the structures and glycosylation patterns of Envs from different subtypes and perform cross-clade statistical analyses to reveal the unique features of CRF01_AE V1 region, which are associated with the resistance to certain bNAbs. We also solve a 4.1 Å cryo-EM structure of CRF01_AE Env in complex with F6, the first bNAb from CRF01_AE-infected individuals. F6 recognizes a gp120-gp41 spanning epitope to allosterically destabilize the Env trimer apex and weaken inter-protomer packing, which in turn hinders the receptor binding and induces Env trimer disassembly, demonstrating a dual mechanism of neutralization. These findings broaden our understanding of CRF Envs and shed lights on immunofocusing HIV-1 vaccine design.
History
DepositionAug 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F6 Fab heavy Chain
B: F6 Fab light chain
C: F6 Fab heavy Chain
D: F6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)98,8874
Polymers98,8874
Non-polymers00
Water00
1
A: F6 Fab heavy Chain
B: F6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,4442
Polymers49,4442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-24 kcal/mol
Surface area20100 Å2
MethodPISA
2
C: F6 Fab heavy Chain
D: F6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,4442
Polymers49,4442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-12 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.245, 62.271, 97.843
Angle α, β, γ (deg.)90.00, 105.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody F6 Fab heavy Chain


Mass: 25333.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody F6 Fab light chain


Mass: 24109.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium citrate, 20% PEG 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.3→19.71 Å / Num. obs: 29265 / % possible obs: 97.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 63.58 Å2 / CC1/2: 0.97 / Rpim(I) all: 0.13 / Rrim(I) all: 0.24 / Net I/σ(I): 6.11
Reflection shellResolution: 3.3→3.5 Å / Num. unique obs: 1352 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BMF

5bmf


Resolution: 3.34→19.71 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2806 2955 10.1 %
Rwork0.2417 --
obs0.2455 29265 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.34→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5758 0 0 0 5758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035875
X-RAY DIFFRACTIONf_angle_d0.7417964
X-RAY DIFFRACTIONf_dihedral_angle_d5.36810
X-RAY DIFFRACTIONf_chiral_restr0.046900
X-RAY DIFFRACTIONf_plane_restr0.0061007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.390.3527910.3573817X-RAY DIFFRACTION63
3.39-3.450.31861560.29851243X-RAY DIFFRACTION97
3.45-3.510.29611300.30331284X-RAY DIFFRACTION100
3.51-3.580.30371260.29111254X-RAY DIFFRACTION98
3.58-3.650.36451690.26591288X-RAY DIFFRACTION100
3.65-3.730.27911260.27471276X-RAY DIFFRACTION100
3.73-3.820.27111620.25711272X-RAY DIFFRACTION100
3.82-3.910.31761150.25171304X-RAY DIFFRACTION100
3.91-4.020.28871500.26031263X-RAY DIFFRACTION100
4.02-4.140.29911480.22711319X-RAY DIFFRACTION100
4.14-4.270.28041560.22891249X-RAY DIFFRACTION99
4.27-4.420.27171350.22471299X-RAY DIFFRACTION98
4.42-4.590.27361390.20571255X-RAY DIFFRACTION100
4.59-4.80.23911620.20391285X-RAY DIFFRACTION100
4.8-5.050.23221510.21311254X-RAY DIFFRACTION100
5.05-5.360.26261300.21391296X-RAY DIFFRACTION100
5.36-5.760.3031490.23931261X-RAY DIFFRACTION98
5.76-6.320.28151410.25561257X-RAY DIFFRACTION99
6.33-7.20.27151400.25441301X-RAY DIFFRACTION100
7.2-8.930.24721380.22821269X-RAY DIFFRACTION98
8.93-19.710.26691410.23021264X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -14.464 Å / Origin y: 15.8549 Å / Origin z: -22.641 Å
111213212223313233
T0.8583 Å2-0.012 Å2-0.2451 Å2-0.5322 Å20.0023 Å2--0.6138 Å2
L0.9815 °20.0137 °2-0.4615 °2--0.1365 °20.0509 °2--0.063 °2
S-0.0207 Å °-0.0809 Å °0.098 Å °-0.0402 Å °0.0598 Å °0.0405 Å °0.1013 Å °0.014 Å °-0.0501 Å °
Refinement TLS groupSelection details: all

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