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- PDB-4lsv: Crystal structure of broadly and potently neutralizing antibody 3... -

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Basic information

Entry
Database: PDB / ID: 4lsv
TitleCrystal structure of broadly and potently neutralizing antibody 3BNC117 in complex with HIV-1 clade C C1086 gp120
Components
  • HEAVY CHAIN OF ANTIBODY 3BNC117
  • LIGHT CHAIN OF ANTIBODY 3BNC117
  • envelope glycoprotein GP120
Keywordsviral protein/immune system / Neutralizing antibody 3BNC117 / 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
IMIDAZOLE / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 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_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 30, 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 3BNC117
L: LIGHT CHAIN OF ANTIBODY 3BNC117
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,93715
Polymers87,4353
Non-polymers2,50212
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint26 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.615, 191.615, 103.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11G-609-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody HEAVY CHAIN OF ANTIBODY 3BNC117


Mass: 24656.484 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): HEK293F / Production host: Homo sapiens (human)
#3: Antibody LIGHT CHAIN OF ANTIBODY 3BNC117


Mass: 23022.658 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): HEK293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 12 molecules G

#1: Protein envelope glycoprotein GP120


Mass: 39755.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: C1086 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: C6G099*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 , 2 types, 78 molecules

#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.1M imidazole, 11% PEG 3350, 0.5M NaCl, 0.2M MgCl2, pH 6.5, 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
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2011
RadiationMonochromator: APD 22-ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 22670 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 53.04 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 17.46
Reflection shellResolution: 2.84→3.02 Å / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3.32 / % possible all: 95.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXdev_998refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.32 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.47 / σ(F): 1.26 / Phase error: 33.13 / Stereochemistry target values: ML
Details: RESIDUE (G ASN 462 ) AND RESIDUE (G ASP 464 ) ARE LINKED TOGETHER
RfactorNum. reflection% reflection
Rfree0.299 1892 5.15 %
Rwork0.26 --
obs0.262 22628 99.2 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.55 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 88.98 Å2
Baniso -1Baniso -2Baniso -3
1--25.6742 Å2-0 Å20 Å2
2---25.6742 Å20 Å2
3---43.7751 Å2
Refinement stepCycle: LAST / Resolution: 3→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5996 0 159 77 6232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026330
X-RAY DIFFRACTIONf_angle_d0.5898598
X-RAY DIFFRACTIONf_dihedral_angle_d11.5952317
X-RAY DIFFRACTIONf_chiral_restr0.038969
X-RAY DIFFRACTIONf_plane_restr0.0031095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0750.41221800.36072469X-RAY DIFFRACTION99
3.075-3.15810.41821430.34042468X-RAY DIFFRACTION99
3.1581-3.2510.35151110.32722488X-RAY DIFFRACTION99
3.251-3.3560.45851070.33322514X-RAY DIFFRACTION99
3.356-3.47590.36971500.31752471X-RAY DIFFRACTION99
3.4759-3.6150.36711340.29312498X-RAY DIFFRACTION99
3.615-3.77940.33711680.29962424X-RAY DIFFRACTION99
3.7794-3.97860.32521360.27592518X-RAY DIFFRACTION99
3.9786-4.22770.28721330.26552484X-RAY DIFFRACTION99
4.2277-4.55390.26241330.22712493X-RAY DIFFRACTION99
4.5539-5.01170.21971410.21082497X-RAY DIFFRACTION99
5.0117-5.73590.29011160.22362510X-RAY DIFFRACTION100
5.7359-7.22250.28551280.23892507X-RAY DIFFRACTION100
7.2225-47.32490.15961120.19192533X-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)
11.01710.5748-0.25611.2430.05210.10840.20830.3003-0.4343-0.39150.2776-0.11120.4252-0.1166-0.08840.595-0.068-0.61890.8109-0.63862.3002-83.1422-73.9563-31.6391
21.2121-0.2134-0.01480.27730.00651.02170.28560.1289-1.1232-0.10130.302-0.21110.2910.5703-0.35720.56030.1533-0.43530.8013-0.56282.1825-63.4572-69.044-20.255
32.774-0.00341.58592.80191.60515.23970.2035-0.4708-1.32660.3233-0.1128-0.09660.2767-0.3242-0.10170.3923-0.0082-0.01420.4130.23770.7361-74.1919-49.2601-5.2822
42.1424-0.7063-1.00961.62950.61175.82170.4588-0.50550.43130.29850.0193-0.0846-1.42170.4576-0.29751.1441-0.13620.13620.78870.05440.2047-66.5136-17.619714.5934
51.7982-0.34010.5572.2793-0.73743.2124-0.13140.32590.1481-0.19380.1723-0.0554-0.5181-0.1893-0.01230.62730.0151-0.03240.50940.01840.0797-79.3904-30.5942-18.9831
62.34970.07690.45821.7518-0.16543.86870.0238-0.24370.01010.2583-0.4834-0.1261-0.19370.68460.27110.9511-0.1103-0.02460.6872-0.07680.1365-57.9727-14.90481.2054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN G AND (RESID 44:253 OR RESID 476:492 ) )
2X-RAY DIFFRACTION2(CHAIN G AND RESID 254:475 )
3X-RAY DIFFRACTION3(CHAIN H AND RESID 1:113 )
4X-RAY DIFFRACTION4(CHAIN H AND RESID 114:213 )
5X-RAY DIFFRACTION5(CHAIN L AND RESID 1:108 )
6X-RAY DIFFRACTION6(CHAIN L AND RESID 109:211 )

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