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- PDB-6chb: Crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-... -

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Basic information

Entry
Database: PDB / ID: 6chb
TitleCrystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and IOMA
Components
  • (Envelope glycoprotein ...) x 2
  • BG18 Heavy Chain
  • BG18 Light Chain
  • IOMA Heavy Chain
  • IOMA Light Chain
KeywordsIMMUNE SYSTEM / Env glycoprotein / broadly neutralizing antibodies
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.801 Å
AuthorsBarnes, C.O. / Bjorkman, P.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI100148 United States
Bill & Melinda Gates FoundationOPP1124068 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural characterization of a highly-potent V3-glycan broadly neutralizing antibody bound to natively-glycosylated HIV-1 envelope.
Authors: Barnes, C.O. / Gristick, H.B. / Freund, N.T. / Escolano, A. / Lyubimov, A.Y. / Hartweger, H. / West, A.P. / Cohen, A.E. / Nussenzweig, M.C. / Bjorkman, P.J.
History
DepositionFeb 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Envelope glycoprotein gp41
G: Envelope glycoprotein gp120
J: BG18 Heavy Chain
K: BG18 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
A: Envelope glycoprotein gp41
F: Envelope glycoprotein gp120
M: IOMA Heavy Chain
N: IOMA Light Chain
I: BG18 Heavy Chain
L: BG18 Light Chain
C: Envelope glycoprotein gp41
H: Envelope glycoprotein gp120
O: IOMA Heavy Chain
P: IOMA Light Chain
Q: BG18 Heavy Chain
R: BG18 Light Chain


Theoretical massNumber of molelcules
Total (without water)503,41418
Polymers503,41418
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49670 Å2
ΔGint-298 kcal/mol
Surface area172360 Å2
Unit cell
Length a, b, c (Å)176.752, 176.752, 458.039
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Envelope glycoprotein ... , 2 types, 6 molecules BACGFH

#1: Protein Envelope glycoprotein gp41 / Env polyprotein


Mass: 17162.525 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pAM/C / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): K1 / References: UniProt: Q2N0S7, UniProt: Q2N0S5*PLUS
#2: Protein Envelope glycoprotein gp120 / Env polyprotein


Mass: 53693.789 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pAM/C / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): K1 / References: UniProt: Q2N0S6

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Protein , 1 types, 3 molecules JIQ

#3: Protein BG18 Heavy Chain


Mass: 26158.375 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Antibody , 3 types, 9 molecules KLRDMOENP

#4: Antibody BG18 Light Chain


Mass: 23021.447 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody IOMA Heavy Chain


Mass: 25176.416 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#6: Antibody IOMA Light Chain


Mass: 22591.975 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)

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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: 3.55 Å3/Da / Density % sol: 65.39 % / Mosaicity: 0.22 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 5% Tacismate pH 8.0, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 6.66→39.7 Å / Num. obs: 13894 / % possible obs: 98.7 % / Redundancy: 12.4 % / Biso Wilson estimate: 368.33 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.333 / Rpim(I) all: 0.097 / Rrim(I) all: 0.347 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
6.66-7.0212.54.75218900.3341.3654.95495
21.07-39.79.60.094300.9930.0290.09583.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimless3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T3Z, 5UD9

5t3z

5ud9


Resolution: 6.801→39.631 Å / SU ML: 1.68 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 51.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4167 639 4.95 %
Rwork0.3179 --
obs0.3232 13121 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6.801→39.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28753 0 0 0 28753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00329442
X-RAY DIFFRACTIONf_angle_d0.71740047
X-RAY DIFFRACTIONf_dihedral_angle_d9.51417578
X-RAY DIFFRACTIONf_chiral_restr0.0454477
X-RAY DIFFRACTIONf_plane_restr0.0065106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.8005-7.10830.44881490.37272800X-RAY DIFFRACTION100
7.1083-7.48070.36641490.34352800X-RAY DIFFRACTION100
7.4807-7.94590.41481530.30872798X-RAY DIFFRACTION99
7.9459-8.55370.46741440.30182805X-RAY DIFFRACTION100
8.5537-9.40410.36561480.28132817X-RAY DIFFRACTION100
9.4041-10.74110.39461290.28292834X-RAY DIFFRACTION100
10.7411-13.44440.36181290.31062833X-RAY DIFFRACTION99
13.4444-39.63170.46691690.35592768X-RAY DIFFRACTION99

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