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

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Basic information

Entry
Database: PDB / ID: 4lss
TitleCrystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade A strain KER_2018_11 gp120
Components
  • HEAVY CHAIN OF ANTIBODY VRC01
  • LIGHT CHAIN OF ANTIBODY VRC01 with N72T mutation
  • envelope glycoprotein GP120
Keywordsviral protein/immune system / antibody antigen complex / Neutralizing antibody VRC01 / 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
ISOPROPYL ALCOHOL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 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 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Oct 9, 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
H: HEAVY CHAIN OF ANTIBODY VRC01
L: LIGHT CHAIN OF ANTIBODY VRC01 with N72T mutation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,64421
Polymers87,3843
Non-polymers3,26018
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.639, 65.267, 259.146
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 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 with N72T mutation


Mass: 23159.688 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)

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Protein / Sugars , 2 types, 13 molecules G

#1: Protein envelope glycoprotein GP120


Mass: 39828.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: KER2018_11 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q3ZLH8*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.: 12
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, 151 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 8% PEG 4000, 6.5% isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 3, 2011
RadiationMonochromator: APS ID22 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 30121 / Num. obs: 27290 / % possible obs: 90.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.127 / Rsym value: 0.098 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.59-2.633.60.727168.9
2.63-2.684.40.667181.7
2.68-2.735.30.731184.3
2.73-2.7960.628188.7
2.79-2.856.50.573186.2
2.85-2.926.90.528188.4
2.92-2.997.10.444188.7
2.99-3.077.10.367188.1
3.07-3.167.20.291186.9
3.16-3.267.20.25188.4
3.26-3.387.10.206189.2
3.38-3.517.10.16189.9
3.51-3.6770.14190.3
3.67-3.8770.115194.4
3.87-4.1170.096197.9
4.11-4.437.20.078199.9
4.43-4.877.40.0721100
4.87-5.587.60.079199.9
5.58-7.027.70.0781100
7.02-507.10.044198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_998refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→32.393 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / σ(F): 0 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 1388 5.1 %
Rwork0.1916 --
obs0.1953 27223 90.88 %
all-29955 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.861 Å2 / ksol: 0.295 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7004 Å2-0 Å20 Å2
2---3.6834 Å20 Å2
3---1.983 Å2
Refinement stepCycle: LAST / Resolution: 2.59→32.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 0 205 145 6316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056330
X-RAY DIFFRACTIONf_angle_d0.8918594
X-RAY DIFFRACTIONf_dihedral_angle_d15.9562342
X-RAY DIFFRACTIONf_chiral_restr0.049972
X-RAY DIFFRACTIONf_plane_restr0.0031083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.586-2.67840.36281120.3082141X-RAY DIFFRACTION77
2.6784-2.78560.36261310.29042404X-RAY DIFFRACTION86
2.7856-2.91230.34611570.25622415X-RAY DIFFRACTION87
2.9123-3.06570.30111120.2232509X-RAY DIFFRACTION88
3.0657-3.25760.31621420.22432467X-RAY DIFFRACTION87
3.2576-3.50890.31141410.20732502X-RAY DIFFRACTION90
3.5089-3.86150.29161290.19432652X-RAY DIFFRACTION93
3.8615-4.41910.22611370.15432821X-RAY DIFFRACTION99
4.4191-5.5630.20151590.14242895X-RAY DIFFRACTION100
5.563-32.39580.21421680.17423029X-RAY DIFFRACTION100
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)
12.8391-1.16271.39813.14530.48834.8041-0.03070.16460.2122-0.2672-0.10630.018-0.4866-0.15740.17460.2314-0.02250.03040.1856-0.00710.2712-12.324718.677254.5757
23.08470.20560.19021.90030.7991.28120.0839-0.1386-0.13640.098-0.14480.25340.171-0.32170.03260.1928-0.02160.03150.234-0.01030.2506-13.7416-3.765356.2981
32.1452-0.3672-0.02672.5902-0.54434.5259-0.00930.03430.11940.0285-0.1217-0.4324-0.17640.5810.07190.1833-0.0064-0.00660.25810.00590.2026.3572-9.075138.3425
42.7751-0.6448-1.97453.84-0.54276.3616-0.1005-0.0425-0.3953-0.00370.024-0.22090.88940.30320.01770.46010.1309-0.02240.31040.01350.39489.7025-38.06938.1601
51.28670.141-0.81973.65591.69766.90680.09430.02490.1222-0.20460.0795-0.2664-0.13550.0923-0.18840.25950.04140.00820.24980.02240.21480.3736-2.796817.0809
65.00522.9799-0.73456.4313-2.06644.51280.1585-0.1484-0.2831-0.1886-0.0460.14770.3373-0.3446-0.12820.3305-0.00410.00560.2789-0.06750.2799-3.3656-30.06044.0953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN G AND ( RESID 44:253 OR RESID 476:492 ) )G44 - 253
2X-RAY DIFFRACTION1( CHAIN G AND ( RESID 44:253 OR RESID 476:492 ) )G476 - 492
3X-RAY DIFFRACTION2( CHAIN G AND RESID 254:475 )G254 - 475
4X-RAY DIFFRACTION3( CHAIN H AND RESID 1:114 )H1 - 114
5X-RAY DIFFRACTION4( CHAIN H AND RESID 115:216 )H115 - 216
6X-RAY DIFFRACTION5( CHAIN L AND RESID 3:108 )L3 - 108
7X-RAY DIFFRACTION6( CHAIN L AND RESID 109:216 )L109 - 216

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