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

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Basic information

Entry
Database: PDB / ID: 4lst
TitleCrystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade C strain ZM176.66 gp120
Components
  • ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
  • HEAVY CHAIN OF ANTIBODY VRC01
  • LIGHT CHAIN OF ANTIBODY VRC01
Keywordsviral protein/immune system / Neutralizing antibody VRC01 / HIV envelope glycoprotein gp120 / antibody antigen / viral protein-immune system complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / 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 GP120 of HIV-1 clade C
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 27, 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 of HIV-1 clade C
H: HEAVY CHAIN OF ANTIBODY VRC01
L: LIGHT CHAIN OF ANTIBODY VRC01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,61111
Polymers86,8423
Non-polymers1,7708
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint7 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.105, 77.981, 200.351
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 C


Mass: 39273.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: ZM176.66 / Gene: env / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: R4GRV3
#2: Antibody HEAVY CHAIN OF ANTIBODY VRC01


Mass: 24395.684 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 VRC01


Mass: 23172.686 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)
#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.: 8
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 0.1M Tris, 11.8% PEG 4000, 0.2M Na-Acetate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, 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: Jan 1, 2011
RadiationMonochromator: APS 22-BM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 32759 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.086 / Net I/σ(I): 10.5
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.321 / % possible all: 56

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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: 2.55→40.68 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 1.36 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1649 5.05 %
Rwork0.19 --
obs0.193 32670 91.9 %
all-35565 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.91 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 104.99 Å2
Baniso -1Baniso -2Baniso -3
1-7.8265 Å20 Å2-0 Å2
2--10.6871 Å2-0 Å2
3----18.5135 Å2
Refinement stepCycle: LAST / Resolution: 2.55→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 112 71 6171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046258
X-RAY DIFFRACTIONf_angle_d0.8968487
X-RAY DIFFRACTIONf_dihedral_angle_d13.0632305
X-RAY DIFFRACTIONf_chiral_restr0.06954
X-RAY DIFFRACTIONf_plane_restr0.0041083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5522-2.62730.3377920.28411618X-RAY DIFFRACTION58
2.6273-2.71210.31531010.28341982X-RAY DIFFRACTION71
2.7121-2.8090.34541340.28332385X-RAY DIFFRACTION87
2.809-2.92140.37231380.27722678X-RAY DIFFRACTION96
2.9214-3.05440.3321390.2622750X-RAY DIFFRACTION99
3.0544-3.21530.32471390.2422805X-RAY DIFFRACTION99
3.2153-3.41670.26241530.22532768X-RAY DIFFRACTION99
3.4167-3.68030.28431260.20882780X-RAY DIFFRACTION100
3.6803-4.05040.27671460.18652799X-RAY DIFFRACTION99
4.0504-4.63580.2181440.14782800X-RAY DIFFRACTION99
4.6358-5.83790.20641630.15732802X-RAY DIFFRACTION98
5.8379-40.6860.19241740.17862854X-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)
13.769-1.82190.82417.3658-2.11474.35970.10350.18930.2463-0.0405-0.212-0.55560.46820.61640.15970.6193-0.07190.07540.8397-0.07180.539834.00786.23096.4288
23.56490.7037-0.40433.7512-1.73966.3759-0.0750.6827-0.1497-0.45210.11420.4140.6567-0.207-0.02850.7244-0.1054-0.01620.6584-0.10240.512311.50293.84925.1994
37.5069-2.0111-0.316.29770.96627.5836-0.0235-0.34220.64160.3291-0.0417-0.0069-0.2435-0.26170.08480.5341-0.0615-0.05350.5177-0.02990.40996.250919.571527.22
49.23592.18241.21297.7928-3.01184.85440.1821-0.329-0.06160.41550.08550.4346-0.1669-0.1626-0.25141.15330.08860.02880.7194-0.06310.6714-21.518419.942659.5296
57.195-1.6998-2.72744.4976-0.54248.0259-0.2817-0.8379-0.10020.81120.1112-0.12930.70490.06710.14680.86090.017-0.0710.6977-0.03110.460513.02529.038846.3702
66.61620.27262.04392.07071.24485.84220.39260.149-0.981-0.05340.36780.30320.9185-0.1082-0.7241.3145-0.0262-0.22810.55970.0080.9336-15.3275.199961.253
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 1:114
4X-RAY DIFFRACTION4chain H and resid 115:216
5X-RAY DIFFRACTION5chain L and resid 1:108
6X-RAY DIFFRACTION6chain L and resid 109:216

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