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- PDB-4ydi: Crystal structure of broad and potently neutralizing VRC01-class ... -

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Basic information

Entry
Database: PDB / ID: 4ydi
TitleCrystal structure of broad and potently neutralizing VRC01-class antibody Z258-VRC27.01, isolated from human donor Z258, in complex with HIV-1 gp120 from clade A strain Q23.17
Components
  • Envelope glycoprotein gp160
  • HEAVY CHAIN OF ANTIBODY Z258-VRC27.01
  • LIGHT CHAIN OF ANTIBODY Z258-VRC27.01
KeywordsIMMUNE SYSTEM / Antibody / HIV-1
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma 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: 3.452 Å
AuthorsZhou, T. / Srivatsan, S. / Kwong, P.D.
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, A.P. / Bjorkman, P.J. / Scheid, J.F. / Nussenzweig, M.C. / Shapiro, L. / Mascola, J.R. / Kwong, P.D.
History
DepositionFeb 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 gp160
H: HEAVY CHAIN OF ANTIBODY Z258-VRC27.01
L: LIGHT CHAIN OF ANTIBODY Z258-VRC27.01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,24821
Polymers87,9263
Non-polymers3,32218
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.738, 172.253, 91.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody HEAVY CHAIN OF ANTIBODY Z258-VRC27.01


Mass: 24897.025 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 Z258-VRC27.01


Mass: 23048.617 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, 14 molecules G

#1: Protein Envelope glycoprotein gp160


Mass: 39980.078 Da / Num. of mol.: 1 / Fragment: UNP residues 43-122, 191-293, 315-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK 293 GNTI- / Production host: Homo sapiens (human) / References: UniProt: O55774
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
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 , 3 types, 24 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 4% PEG 400, 1.9 M (NH4)2SO4, 0.1M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. obs: 13262 / % possible obs: 87.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 80.69 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.064 / Rrim(I) all: 0.157 / Χ2: 1.688 / Net I/av σ(I): 11.507 / Net I/σ(I): 7.8 / Num. measured all: 72734
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.45-3.573.50.3488600.8630.1770.3951.30258.1
3.57-3.723.80.36910360.890.190.4191.30569.3
3.72-3.894.20.42911610.880.2160.4841.31778.8
3.89-4.094.80.33512600.9440.1590.3721.44884.2
4.09-4.355.10.24513440.9730.1120.271.57989.7
4.35-4.685.60.1814440.9910.0790.1971.73995.6
4.68-5.1560.16614950.9910.0720.1811.69398.9
5.15-5.96.50.17815140.990.0750.1941.62899.9
5.9-7.4370.13715390.9940.0560.1481.60399.9
7.43-506.40.05316090.9980.0220.0582.3899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE9

3se9


Resolution: 3.452→46.038 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 675 5.11 %Random selection
Rwork0.222 12540 --
obs0.2246 13215 87.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 268.62 Å2 / Biso mean: 112.7391 Å2 / Biso min: 28.47 Å2
Refinement stepCycle: final / Resolution: 3.452→46.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5944 0 206 19 6169
Biso mean--140.4 68.69 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046309
X-RAY DIFFRACTIONf_angle_d1.0218600
X-RAY DIFFRACTIONf_chiral_restr0.045985
X-RAY DIFFRACTIONf_plane_restr0.0051089
X-RAY DIFFRACTIONf_dihedral_angle_d12.3842316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.452-3.71840.35191050.29581757186263
3.7184-4.09240.32351250.26092297242282
4.0924-4.6840.23641480.19052631277992
4.684-5.89940.281480.20322860300899
5.8994-46.0420.25581490.220329953144100
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)
12.6959-0.298-0.11473.853-2.24553.0172-0.2056-1.24910.33891.95280.32630.6935-0.251-0.0647-0.09981.690.32670.60861.191-0.0681.2182-56.9152-8.535329.5937
23.89330.01830.6076.8246-0.26074.3717-0.1417-0.85920.06591.48730.3699-0.52380.0620.3391-0.22170.76240.1963-0.04130.7802-0.09950.7921-39.4521-13.158222.529
37.469-4.16621.2622.5303-1.29994.3022-0.1605-0.29690.62670.70080.2862-0.9154-0.28450.3756-0.01760.4997-0.0668-0.04760.5413-0.05490.7289-40.3079-6.227611.0914
45.62250.2913-0.7235.6003-1.81034.3699-0.0526-0.33940.20340.97320.1643-0.2233-0.44420.31930.03960.70680.1402-0.16770.693-0.16830.4962-41.4401-18.386318.576
59.45060.286-5.90596.14521.57178.74320.31660.90970.5445-0.53710.06771.5369-0.7911-1.342-0.37880.52440.0559-0.13760.59970.0690.9852-57.6806-23.7168-5.9211
60.92482.02350.12614.4920.94677.078-0.2588-0.5889-0.0392-0.32110.1464-0.51960.76910.7579-0.22880.24790.028-0.20740.6034-0.0250.852-49.6072-31.5227-1.2913
76.2496-0.5339-3.60416.00444.05084.4050.1722-0.1184-0.1183-0.54390.39250.42930.12750.1074-0.4120.70580.1005-0.23860.58260.30060.6236-44.9965-21.7851.1112
83.19452.3627-2.20175.32153.44518.92850.61670.32940.1517-0.8765-0.47080.24930.1104-0.5755-0.23660.8067-0.0039-0.19880.48860.09020.9047-50.9007-21.1517-6.9497
94.8334-1.8987-1.41674.10431.02187.7694-0.3097-0.45380.03091.14340.66741.7145-0.7625-0.9138-0.18020.76780.16690.08790.53060.09781.0183-56.6985-29.6585.5915
100.65020.38810.49881.01310.84671.09630.40540.8301-0.2903-0.8934-0.08750.5820.56530.1598-0.06431.1151-0.0462-0.8251.18570.30990.5159-54.0873-34.9606-19.745
110.22230.0694-0.23571.8953-0.59480.40580.47940.5887-0.4533-0.47350.11840.35810.28980.3125-0.30152.38560.3574-0.61930.9265-0.07420.8511-54.2654-41.0014-29.7692
120.941-0.21490.32980.0952-0.22910.39870.11121.5911-0.415-0.58310.00470.3241-0.1857-0.6197-0.35461.65240.2041-1.86361.5834-0.20561.1373-60.3484-47.9527-32.7075
138.27321.77691.64013.1822-0.09023.37330.5684-0.2191-0.72990.19630.0119-0.23360.21390.0998-0.25010.35550.1714-0.50680.787-0.00011.762-52.1876-52.80663.0673
144.21883.7351.44974.16343.44375.9234-0.6722-0.54181.4013-0.0342-0.42630.7603-1.1249-0.33661.08770.85690.2168-0.30450.7410.01551.3702-48.1871-46.405312.2688
156.4715-2.0239-0.23845.2313-1.99369.44350.06750.4003-0.7311-0.2162-0.1711.04730.0903-0.51080.12080.39240.13140.03570.66390.28521.2599-59.1383-41.75763.893
165.41922.22241.26345.99350.71385.2138-0.1043-0.0978-0.70370.79190.3851.06660.4327-0.2964-0.30420.46940.18470.1490.56190.12411.409-57.7576-48.45135.2087
175.29281.9962-3.37415.1388-3.98633.760.50851.13390.0934-1.0267-0.2630.5247-1.0276-1.0503-0.13292.06790.3314-0.59590.9639-0.25831.0691-50.2909-55.9328-27.9349
187.84863.50632.28117.2152-2.61962.99870.27621.2616-0.2552-2.6224-0.20.1620.60210.4078-0.07542.18970.2328-0.38771.232-0.37020.8417-37.4752-58.2614-25.4966
192.211-1.21950.23382.0786-0.13322.47240.2781.1106-1.1995-1.5822-0.66740.77640.275-0.50370.4151.99310.2351-0.50340.8627-0.30981.2056-46.2002-54.4033-25.7924
207.742.0946-2.4733.3295-0.35576.7719-0.66421.079-1.6964-1.7865-0.769-0.1793-0.5072-0.04471.31651.72240.344-0.24210.852-0.27831.219-45.273-65.2585-26.0167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 44 through 235 )G0
2X-RAY DIFFRACTION2chain 'G' and (resid 236 through 353 )G0
3X-RAY DIFFRACTION3chain 'G' and (resid 354 through 446 )G0
4X-RAY DIFFRACTION4chain 'G' and (resid 447 through 492 )G0
5X-RAY DIFFRACTION5chain 'H' and (resid 2 through 33 )H0
6X-RAY DIFFRACTION6chain 'H' and (resid 34 through 52 )H0
7X-RAY DIFFRACTION7chain 'H' and (resid 52A through 66 )H0
8X-RAY DIFFRACTION8chain 'H' and (resid 67 through 87 )H0
9X-RAY DIFFRACTION9chain 'H' and (resid 88 through 100D)H0
10X-RAY DIFFRACTION10chain 'H' and (resid 100E through 124 )H0
11X-RAY DIFFRACTION11chain 'H' and (resid 138 through 150 )H0
12X-RAY DIFFRACTION12chain 'H' and (resid 151 through 214 )H0
13X-RAY DIFFRACTION13chain 'L' and (resid 2 through 18 )L0
14X-RAY DIFFRACTION14chain 'L' and (resid 19 through 33 )L0
15X-RAY DIFFRACTION15chain 'L' and (resid 34 through 53 )L0
16X-RAY DIFFRACTION16chain 'L' and (resid 54 through 108 )L0
17X-RAY DIFFRACTION17chain 'L' and (resid 109 through 143 )L0
18X-RAY DIFFRACTION18chain 'L' and (resid 144 through 155 )L0
19X-RAY DIFFRACTION19chain 'L' and (resid 156 through 198 )L0
20X-RAY DIFFRACTION20chain 'L' and (resid 199 through 214 )L0

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