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- PDB-4ye4: Crystal Structure of Neutralizing Antibody HJ16 in Complex with H... -

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Basic information

Entry
Database: PDB / ID: 4ye4
TitleCrystal Structure of Neutralizing Antibody HJ16 in Complex with HIV-1 gp120
Components
  • HT593.1 gp120
  • Heavy chain human antibody HJ16
  • Light chain of HJ16
KeywordsViral protein/Immune system / HIV1 / antibody / gp120 / complex / Viral protein-Immune system complex
Function / homology
Function and homology information


: / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / 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
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsKwong, P.D. / Chen, L. / Zhou, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell / Year: 2015
Title: Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors.
Authors: Zhou, T. / Lynch, R.M. / Chen, L. / Acharya, P. / Wu, X. / Doria-Rose, N.A. / Joyce, M.G. / Lingwood, D. / Soto, C. / Bailer, R.T. / Ernandes, M.J. / Kong, R. / Longo, N.S. / Louder, M.K. / ...Authors: Zhou, T. / Lynch, R.M. / Chen, L. / Acharya, P. / Wu, X. / Doria-Rose, N.A. / Joyce, M.G. / Lingwood, D. / Soto, C. / Bailer, R.T. / Ernandes, M.J. / Kong, R. / Longo, N.S. / Louder, M.K. / McKee, K. / O'Dell, S. / Schmidt, S.D. / Tran, L. / Yang, Z. / Druz, A. / Luongo, T.S. / Moquin, S. / Srivatsan, S. / Yang, Y. / Zhang, B. / Zheng, A. / Pancera, M. / Kirys, T. / Georgiev, I.S. / Gindin, T. / Peng, H.P. / Yang, A.S. / Mullikin, J.C. / Gray, M.D. / Stamatatos, L. / Burton, D.R. / Koff, W.C. / Cohen, M.S. / Haynes, B.F. / Casazza, J.P. / Connors, M. / Corti, D. / Lanzavecchia, A. / Sattentau, Q.J. / Weiss, R.A. / West Jr., A.P. / Bjorkman, P.J. / Scheid, J.F. / Nussenzweig, M.C. / Shapiro, L. / Mascola, J.R. / Kwong, P.D.
History
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Experimental preparation
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 4, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_abbrev ..._chem_comp.type / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Mar 30, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: HT593.1 gp120
H: Heavy chain human antibody HJ16
L: Light chain of HJ16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,07211
Polymers88,3023
Non-polymers1,7708
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint7 kcal/mol
Surface area35060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.712, 99.037, 180.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein HT593.1 gp120


Mass: 39492.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HIV-1 clade B gp120 core / Source: (gene. exp.) Human immunodeficiency virus / Production host: Homo sapiens (human) / References: UniProt: Q69994*PLUS
#2: Antibody Heavy chain human antibody HJ16


Mass: 24606.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Light chain of HJ16


Mass: 24202.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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.: 27 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M imidazole pH 6.5 10 % (W/V) PEG 8000 5% isopropanol
PH range: 6-7

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 14, 2013
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→41.9 Å / Num. obs: 20510 / % possible obs: 94.4 % / Redundancy: 4.6 % / Net I/σ(I): 1.98
Reflection shellHighest resolution: 2.72 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→41.9 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 1025 5 %
Rwork0.1868 --
obs0.1896 20494 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.81 Å2 / Biso mean: 60.9245 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.72→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6027 0 112 27 6166
Biso mean--85.24 44.15 -
Num. residues----778
LS refinement shellHighest resolution: 2.72 Å
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)
15.6398-1.8202-1.45693.27490.35923.95580.07260.4418-0.015-0.232-0.10430.2015-0.078-0.39990.03070.3963-0.0239-0.11060.4270.04090.3475-25.405631.7479-25.0921
22.80030.2412-0.56772.3794-0.25623.21180.1103-0.1581-0.0213-0.0691-0.09340.0897-0.12270.16690.00010.34610.013-0.09020.29970.07440.374-14.010231.9804-6.333
31.0803-0.14690.21531.0766-0.55911.7527-0.00440.0453-0.0947-0.03250.08860.07660.01630.0041-0.03250.2078-0.01210.03030.3058-0.0110.2909-13.16924.563127.803
44.71382.58130.06464.41160.59282.86940.005-0.4903-0.81750.1484-0.003-0.30250.38020.09320.06390.32580.007-0.04980.37090.18780.4486-12.2658-16.292648.0228
52.35822.6571-0.64834.6458-1.41451.93080.0628-0.1519-0.2469-0.06070.0930.32710.069-0.1928-0.13220.2565-0.0012-0.04150.35930.00360.4256-32.20851.746617.7194
63.23631.53152.21662.30931.3854.8821-0.1093-0.58810.25070.16850.17120.5732-0.3714-0.8022-0.02590.44140.0270.09340.65050.19760.5032-28.5622-9.060851.8469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain G and resid 46:256 or chain G and resid 473:492G0
2X-RAY DIFFRACTION2chain G and resid 257:472G257 - 472
3X-RAY DIFFRACTION3chain H and resid 2:185H2 - 185
4X-RAY DIFFRACTION4chain H and resid 186:228H186 - 228
5X-RAY DIFFRACTION5chain L and resid 2:115L2 - 115
6X-RAY DIFFRACTION6chain L and resid 117:218L117 - 218

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