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- PDB-4xvt: Crystal structure of HIV-1 93TH057 coreE gp120 with antibody 45-V... -

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Basic information

Entry
Database: PDB / ID: 4xvt
TitleCrystal structure of HIV-1 93TH057 coreE gp120 with antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995)
Components
  • 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Light chain
  • ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE A/E
  • donor 45 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Heavy chain
KeywordsViral protein/Immune System / HIV-1 antibodyomics neutralizing antibody germline binding / Viral protein-Immune System complex
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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsJoyce, M.G. / Mascola, J.R. / Kwong, P.D.
CitationJournal: Cell / Year: 2015
Title: Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.
Authors: Wu, X. / Zhang, Z. / Schramm, C.A. / Joyce, M.G. / Do Kwon, Y. / Zhou, T. / Sheng, Z. / Zhang, B. / O'Dell, S. / McKee, K. / Georgiev, I.S. / Chuang, G.Y. / Longo, N.S. / Lynch, R.M. / ...Authors: Wu, X. / Zhang, Z. / Schramm, C.A. / Joyce, M.G. / Do Kwon, Y. / Zhou, T. / Sheng, Z. / Zhang, B. / O'Dell, S. / McKee, K. / Georgiev, I.S. / Chuang, G.Y. / Longo, N.S. / Lynch, R.M. / Saunders, K.O. / Soto, C. / Srivatsan, S. / Yang, Y. / Bailer, R.T. / Louder, M.K. / Mullikin, J.C. / Connors, M. / Kwong, P.D. / Mascola, J.R. / Shapiro, L.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
G: ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE A/E
H: donor 45 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Heavy chain
L: 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,54114
Polymers87,1083
Non-polymers2,43311
Water11,259625
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint12 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.647, 67.841, 199.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE A/E


Mass: 39211.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS
#2: Antibody donor 45 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Heavy chain


Mass: 24737.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Light chain


Mass: 23159.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Na Cacodylate pH 6.5, 12% PEG 8000, 0.16 M NaAcetate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→34.11 Å / Num. obs: 97827 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 35.97 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.08 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGB

3ngb


Resolution: 1.69→34.106 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 4882 4.99 %RANDOM
Rwork0.1811 ---
obs0.1831 97823 98.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→34.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6015 0 154 625 6794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176354
X-RAY DIFFRACTIONf_angle_d1.8238632
X-RAY DIFFRACTIONf_dihedral_angle_d15.3642306
X-RAY DIFFRACTIONf_chiral_restr0.096985
X-RAY DIFFRACTIONf_plane_restr0.011108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6903-1.70950.30351060.30462201X-RAY DIFFRACTION70
1.7095-1.72960.39811590.29143043X-RAY DIFFRACTION100
1.7296-1.75070.32111650.26993109X-RAY DIFFRACTION100
1.7507-1.77280.28941560.26673077X-RAY DIFFRACTION100
1.7728-1.79620.29781670.25693103X-RAY DIFFRACTION100
1.7962-1.82080.29531660.24773049X-RAY DIFFRACTION100
1.8208-1.84680.29271710.24463121X-RAY DIFFRACTION100
1.8468-1.87430.29921570.24293094X-RAY DIFFRACTION100
1.8743-1.90360.26261680.233105X-RAY DIFFRACTION100
1.9036-1.93480.30251590.22053061X-RAY DIFFRACTION100
1.9348-1.96820.27271440.20593133X-RAY DIFFRACTION100
1.9682-2.0040.26571710.2063115X-RAY DIFFRACTION100
2.004-2.04250.25181430.21043122X-RAY DIFFRACTION100
2.0425-2.08420.26121600.20733122X-RAY DIFFRACTION100
2.0842-2.12950.24951480.20113113X-RAY DIFFRACTION100
2.1295-2.17910.24251530.19173150X-RAY DIFFRACTION100
2.1791-2.23350.25561830.19273074X-RAY DIFFRACTION100
2.2335-2.29390.22061560.19443112X-RAY DIFFRACTION100
2.2939-2.36140.27271840.1943094X-RAY DIFFRACTION100
2.3614-2.43760.2451730.19733127X-RAY DIFFRACTION100
2.4376-2.52470.26331690.20053134X-RAY DIFFRACTION100
2.5247-2.62570.2431700.19813120X-RAY DIFFRACTION100
2.6257-2.74520.24621780.19483117X-RAY DIFFRACTION100
2.7452-2.88990.28231720.19273130X-RAY DIFFRACTION100
2.8899-3.07080.21181560.18773187X-RAY DIFFRACTION100
3.0708-3.30770.21181630.1793147X-RAY DIFFRACTION100
3.3077-3.64030.19921880.16313171X-RAY DIFFRACTION100
3.6403-4.16620.18431850.15233183X-RAY DIFFRACTION100
4.1662-5.24590.1611440.13873281X-RAY DIFFRACTION100
5.2459-34.11260.21151680.18083346X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -36.6069 Å / Origin y: -12.8401 Å / Origin z: -22.9555 Å
111213212223313233
T0.2196 Å20.0118 Å2-0.0146 Å2-0.2257 Å20.0079 Å2--0.2524 Å2
L0.3604 °20.2561 °20.4312 °2-0.8686 °20.956 °2--1.4675 °2
S-0.0333 Å °-0.0118 Å °0.0304 Å °-0.0517 Å °-0.0982 Å °0.1103 Å °-0.0877 Å °-0.1206 Å °0.1196 Å °
Refinement TLS groupSelection details: all

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