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- PDB-4lsr: Crystal structure of broadly and potently neutralizing antibody V... -

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Basic information

Entry
Database: PDB / ID: 4lsr
TitleCrystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E stran 93TH057 gp120 with LOOP D and Loop V5 from clade A strain KER_2018_11
Components
  • ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN ker_2018_11
  • HEAVY CHAIN OF ANTIBODY VRC-CH31
  • LIGHT CHAIN OF ANTIBODY VRC-CH31 (N70D MUTATION)
Keywordsviral protein/immune system / Neutralizing antibody VRC-CH31 / 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 ...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 / molecular replacement / Resolution: 2.28 Å
AuthorsZhou, T. / Moquin, S. / Kwong, P.D.
CitationJournal: Immunity / Year: 2013
Title: Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies.
Authors: Zhou, T. / Zhu, J. / Wu, X. / Moquin, S. / Zhang, B. / Acharya, P. / Georgiev, I.S. / Altae-Tran, H.R. / Chuang, G.Y. / Joyce, M.G. / Do Kwon, Y. / Longo, N.S. / Louder, M.K. / Luongo, T. / ...Authors: Zhou, T. / Zhu, J. / Wu, X. / Moquin, S. / Zhang, B. / Acharya, P. / Georgiev, I.S. / Altae-Tran, H.R. / Chuang, G.Y. / Joyce, M.G. / Do Kwon, Y. / Longo, N.S. / Louder, M.K. / Luongo, T. / McKee, K. / Schramm, C.A. / Skinner, J. / Yang, Y. / Yang, Z. / Zhang, Z. / Zheng, A. / Bonsignori, M. / Haynes, B.F. / Scheid, J.F. / Nussenzweig, M.C. / Simek, M. / Burton, D.R. / Koff, W.C. / Mullikin, J.C. / Connors, M. / Shapiro, L. / Nabel, G.J. / Mascola, J.R. / Kwong, P.D.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3May 7, 2014Group: Other
Revision 1.4Jul 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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 WITH LOOP D AND V5 FROM STRAIN ker_2018_11
H: HEAVY CHAIN OF ANTIBODY VRC-CH31
L: LIGHT CHAIN OF ANTIBODY VRC-CH31 (N70D MUTATION)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,45417
Polymers87,9833
Non-polymers2,47114
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.934, 67.726, 220.120
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 VRC-CH31


Mass: 25571.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Antibody LIGHT CHAIN OF ANTIBODY VRC-CH31 (N70D MUTATION)


Mass: 22854.301 Da / Num. of mol.: 1 / Mutation: N70D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 10 molecules G

#1: Protein ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN ker_2018_11


Mass: 39556.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: 93TH057 / Gene: ENV / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / 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.: 9
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 , 2 types, 229 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 0.1M Tris, 11% PEG 4000, 0.2 M Li2SO4, pH 8.5, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2011
RadiationMonochromator: APS BM22 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 41144 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.11 / Net I/σ(I): 9.9
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.602 / % possible all: 75

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_998refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→39.5 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / σ(F): 1.35 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 2069 5.05 %
Rwork0.194 --
obs0.198 40990 90.5 %
all-453179 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.75 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 78.32 Å2
Baniso -1Baniso -2Baniso -3
1-22.9363 Å2-0 Å2-0 Å2
2---11.9228 Å2-0 Å2
3----11.0135 Å2
Refinement stepCycle: LAST / Resolution: 2.28→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5941 0 151 224 6316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056244
X-RAY DIFFRACTIONf_angle_d0.8548469
X-RAY DIFFRACTIONf_dihedral_angle_d14.0782275
X-RAY DIFFRACTIONf_chiral_restr0.048963
X-RAY DIFFRACTIONf_plane_restr0.0031076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2789-2.33190.32371230.24512103X-RAY DIFFRACTION75
2.3319-2.39020.3541130.25742251X-RAY DIFFRACTION80
2.3902-2.45480.33621140.2432336X-RAY DIFFRACTION83
2.4548-2.5270.29951310.23212415X-RAY DIFFRACTION85
2.527-2.60860.28021150.24242457X-RAY DIFFRACTION85
2.6086-2.70180.36631450.24492420X-RAY DIFFRACTION87
2.7018-2.80990.28431140.222484X-RAY DIFFRACTION87
2.8099-2.93780.29321270.2122590X-RAY DIFFRACTION90
2.9378-3.09260.25981410.20682638X-RAY DIFFRACTION93
3.0926-3.28630.27281750.20892718X-RAY DIFFRACTION97
3.2863-3.53990.28741550.20222783X-RAY DIFFRACTION97
3.5399-3.89580.24421460.17662855X-RAY DIFFRACTION99
3.8958-4.45890.21411600.15362883X-RAY DIFFRACTION99
4.4589-5.61520.20611450.15382933X-RAY DIFFRACTION100
5.6152-39.50560.24581650.20583055X-RAY DIFFRACTION99
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)
12.7263-0.81482.39533.4836-0.63134.04540.03960.08630.0084-0.1187-0.04190.3319-0.1648-0.14910.00580.25280.01260.14440.24030.00480.4253-13.020.402347.6568
22.1569-0.48610.71252.36160.20773.1384-0.0023-0.095-0.20850.1462-0.02180.66020.4424-0.4206-0.02370.32-0.06190.13830.2636-0.00920.5785-15.7102-21.807249.2238
34.0929-2.6019-1.40983.59431.7233.63760.24740.27210.0933-1.0522-0.292-0.1575-0.28290.13040.10180.61060.02790.09830.26840.03840.29812.0139-27.524428.0974
41.8192-0.3127-1.70971.2053-1.37484.22070.25990.12030.3653-0.51990.2366-0.5398-1.37120.6078-0.50311.3474-0.24640.36890.593-0.15960.647718.9239-41.72811.924
50.4809-0.33510.80881.3453-0.03532.50970.55080.64910.29-1.6767-0.79790.3229-0.3779-0.6904-0.08981.97930.7004-0.0380.74860.17640.3302-7.5961-17.44259.5981
63.8841-0.7279-1.36255.81711.08243.04290.37060.9707-0.3419-0.5944-0.31450.5783-0.9169-0.727-0.02061.37770.19220.01070.7713-0.16310.52725.5687-45.643-7.409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN G AND ( RESID 44:252 OR RESID 474:492 ) )G44 - 252
2X-RAY DIFFRACTION1( CHAIN G AND ( RESID 44:252 OR RESID 474:492 ) )G474 - 492
3X-RAY DIFFRACTION2( CHAIN G AND RESID 253:473 )G253 - 473
4X-RAY DIFFRACTION3( CHAIN H AND RESID 1:118 )H1 - 118
5X-RAY DIFFRACTION4( CHAIN H AND RESID 119:213 )H119 - 213
6X-RAY DIFFRACTION5( CHAIN L AND RESID 1:108 )L1 - 108
7X-RAY DIFFRACTION6( CHAIN L AND RESID 109:212 )L109 - 212

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