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- PDB-3se8: Crystal structure of broadly and potently neutralizing antibody V... -

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Basic information

Entry
Database: PDB / ID: 3se8
TitleCrystal structure of broadly and potently neutralizing antibody VRC03 in complex with HIV-1 gp120
Components
  • HIV-1 Clade AE strain 93TH057 gp120
  • Heavy chain of antibody VRC03
  • Light chain of antibody VRC03
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / GP120 / ANTIBODY / VRC03 / NEUTRALIZATION / VACCINE / ENVELOPE GLYCOPROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / 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: 1.895 Å
AuthorsKwong, P.D. / Zhou, T.
CitationJournal: Science / Year: 2011
Title: Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing.
Authors: Wu, X. / Zhou, T. / Zhu, J. / Zhang, B. / Georgiev, I. / Wang, C. / Chen, X. / Longo, N.S. / Louder, M. / McKee, K. / O'Dell, S. / Perfetto, S. / Schmidt, S.D. / Shi, W. / Wu, L. / Yang, Y. ...Authors: Wu, X. / Zhou, T. / Zhu, J. / Zhang, B. / Georgiev, I. / Wang, C. / Chen, X. / Longo, N.S. / Louder, M. / McKee, K. / O'Dell, S. / Perfetto, S. / Schmidt, S.D. / Shi, W. / Wu, L. / Yang, Y. / Yang, Z.Y. / Yang, Z. / Zhang, Z. / Bonsignori, M. / Crump, J.A. / Kapiga, S.H. / Sam, N.E. / Haynes, B.F. / Simek, M. / Burton, D.R. / Koff, W.C. / Doria-Rose, N.A. / Connors, M. / Mullikin, J.C. / Nabel, G.J. / Roederer, M. / Shapiro, L. / Kwong, P.D. / Mascola, J.R.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Aug 15, 2012Group: Other
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 7, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
G: HIV-1 Clade AE strain 93TH057 gp120
H: Heavy chain of antibody VRC03
L: Light chain of antibody VRC03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,10125
Polymers87,6533
Non-polymers3,44822
Water11,584643
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.010, 70.259, 217.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain of antibody VRC03


Mass: 25294.525 Da / Num. of mol.: 1 / Fragment: Antigen binding fragement of antibody heavy chain
Source method: isolated from a genetically manipulated source
Details: Co-transfection of both heavy and light chain plasmids
Source: (gene. exp.) Homo sapiens (human) / Gene: antibody VRC03 heavy chain / Plasmid: CMVR derived plasmids for IgG1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody Light chain of antibody VRC03


Mass: 23146.795 Da / Num. of mol.: 1 / Fragment: antibody light chain
Source method: isolated from a genetically manipulated source
Details: Co-transfection of both heavy and light chain plasmids
Source: (gene. exp.) Homo sapiens (human) / Gene: antibody VRC03 light chain / Plasmid: CMVR derived plasmids for IgG1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 12 molecules G

#1: Protein HIV-1 Clade AE strain 93TH057 gp120


Mass: 39211.434 Da / Num. of mol.: 1 / Fragment: Core gp120 with truncations
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: 93TH057 / Gene: gp120 / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 4 types, 654 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 54.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 9 % PEG 4000, 200 mM Li2SO4, 100 mM Tris/Cl-, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.895→50 Å / Num. all: 76674 / Num. obs: 69237 / % possible obs: 90.3 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_755)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.895→37.032 Å / SU ML: 0.56 / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 3470 5.02 %RANDOM
Rwork0.1869 ---
obs0.1893 69130 90.21 %-
all-76632 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.82 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7272 Å20 Å2-0 Å2
2--2.6955 Å2-0 Å2
3----3.4227 Å2
Refinement stepCycle: LAST / Resolution: 1.895→37.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6052 0 210 643 6905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056424
X-RAY DIFFRACTIONf_angle_d0.9718716
X-RAY DIFFRACTIONf_dihedral_angle_d13.562340
X-RAY DIFFRACTIONf_chiral_restr0.058977
X-RAY DIFFRACTIONf_plane_restr0.0041099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8946-1.92060.3744630.30991452X-RAY DIFFRACTION51
1.9206-1.9480.3626850.28791706X-RAY DIFFRACTION59
1.948-1.97710.3507980.26992032X-RAY DIFFRACTION71
1.9771-2.0080.34031210.24842228X-RAY DIFFRACTION76
2.008-2.04090.30231200.23682396X-RAY DIFFRACTION84
2.0409-2.07610.30131230.23852578X-RAY DIFFRACTION88
2.0761-2.11390.28331470.23342618X-RAY DIFFRACTION92
2.1139-2.15450.27351470.22292713X-RAY DIFFRACTION95
2.1545-2.19850.30321570.21442757X-RAY DIFFRACTION95
2.1985-2.24630.30121630.21152736X-RAY DIFFRACTION97
2.2463-2.29850.23841260.1982781X-RAY DIFFRACTION95
2.2985-2.3560.28391550.19942781X-RAY DIFFRACTION97
2.356-2.41970.27811330.20472765X-RAY DIFFRACTION95
2.4197-2.49090.26341500.21692763X-RAY DIFFRACTION95
2.4909-2.57120.30291570.2122754X-RAY DIFFRACTION96
2.5712-2.66310.26061580.20032803X-RAY DIFFRACTION97
2.6631-2.76970.26561350.19472793X-RAY DIFFRACTION96
2.7697-2.89570.26761520.19372812X-RAY DIFFRACTION96
2.8957-3.04830.23481430.18352803X-RAY DIFFRACTION96
3.0483-3.23920.25231420.18982853X-RAY DIFFRACTION96
3.2392-3.48910.21581670.19322828X-RAY DIFFRACTION97
3.4891-3.83990.2061510.17822886X-RAY DIFFRACTION98
3.8399-4.39480.191520.15092910X-RAY DIFFRACTION98
4.3948-5.5340.17911590.14152939X-RAY DIFFRACTION98
5.534-37.03870.22571660.19992973X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.77610.62520.86292.6435-0.20752.9362-0.0855-0.09690.1073-0.1284-0.0748-0.0513-0.33320.03260.15960.42160.03660.02750.2920.03360.188111.746432.8725-45.5744
22.26050.30420.14432.6612-0.89711.8881-0.00040.2189-0.1441-0.7281-0.1831-0.45790.57930.46020.04610.48090.12980.13210.22950.00350.130614.597510.0052-46.7129
32.02360.596-0.28333.2854-0.20813.6885-0.11040.16050.1068-0.2138-0.0320.127-0.1098-0.17840.13770.3250.0315-0.01030.2348-0.00620.1629-6.73747.0051-29.1768
45.6716-1.3236-2.91924.33151.53725.5917-0.215-0.26940.02830.19750.13690.28520.2326-0.2470.08340.3332-0.0274-0.00990.17440.03790.2806-27.7564-8.8758-2.9054
52.41010.6991-1.30492.2758-0.0183.89460.1421-0.12730.24030.1824-0.09750.0389-0.2135-0.0393-0.04620.2701-0.0097-0.0240.1525-0.0120.1753-0.911215.5559-7.9376
61.69650.39570.20584.09620.53861.3631-0.0381-0.223-0.21270.37190.1129-0.09610.1498-0.0242-0.06940.44090.020.02860.27460.06190.2204-15.7932-12.38157.7226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain G and (resid 44:253 or resid 476:492)
2X-RAY DIFFRACTION2chain G and resid 254:475
3X-RAY DIFFRACTION3chain H and resid 1:113
4X-RAY DIFFRACTION4chain H and resid 114:214
5X-RAY DIFFRACTION5chain L and resid 1:109
6X-RAY DIFFRACTION6chain L and resid 110:213

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