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- PDB-5te7: Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6... -

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Basic information

Entry
Database: PDB / ID: 5te7
TitleCrystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade C Strain DU172.17 gp120 Core
Components
  • HIV-1 gp120 core
  • Heavy chain of N6
  • Light chain of N6
KeywordsIMMUNE SYSTEM / HIV-1 / VRC01-class Antibody / N6 / CD4-binding site / gp120
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 ...: / 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 speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsZhou, T. / Kwong, P.D.
CitationJournal: Immunity / Year: 2016
Title: Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth.
Authors: Huang, J. / Kang, B.H. / Ishida, E. / Zhou, T. / Griesman, T. / Sheng, Z. / Wu, F. / Doria-Rose, N.A. / Zhang, B. / McKee, K. / O'Dell, S. / Chuang, G.Y. / Druz, A. / Georgiev, I.S. / ...Authors: Huang, J. / Kang, B.H. / Ishida, E. / Zhou, T. / Griesman, T. / Sheng, Z. / Wu, F. / Doria-Rose, N.A. / Zhang, B. / McKee, K. / O'Dell, S. / Chuang, G.Y. / Druz, A. / Georgiev, I.S. / Schramm, C.A. / Zheng, A. / Joyce, M.G. / Asokan, M. / Ransier, A. / Darko, S. / Migueles, S.A. / Bailer, R.T. / Louder, M.K. / Alam, S.M. / Parks, R. / Kelsoe, G. / Von Holle, T. / Haynes, B.F. / Douek, D.C. / Hirsch, V. / Seaman, M.S. / Shapiro, L. / Mascola, J.R. / Kwong, P.D. / Connors, M.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references / Structure summary
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / 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 / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 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
H: Heavy chain of N6
L: Light chain of N6
G: HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,02320
Polymers86,3423
Non-polymers2,68117
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.675, 65.547, 241.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Heavy chain of N6


Mass: 24188.283 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): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light chain of N6


Mass: 23164.713 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): HEK293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 9 molecules G

#3: Protein HIV-1 gp120 core


Mass: 38989.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q202J8*PLUS
#6: 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.: 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

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Non-polymers , 3 types, 324 molecules

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


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7 % w/v PEG 4000, 4 % (v/v) isopropanol, 2 % (v/v) benzamidine, 0.1 M HEPES, pH 7.5

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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: Mar 12, 2015
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 52871 / % possible obs: 96.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.052 / Rrim(I) all: 0.11 / Χ2: 2.347 / Net I/av σ(I): 28.325 / Net I/σ(I): 9.8 / Num. measured all: 223202
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.15-2.193.10.5480.706190.2
2.19-2.233.60.5740.758193.7
2.23-2.273.90.5380.773193.4
2.27-2.324.10.5020.81194.5
2.32-2.374.30.470.832194.8
2.37-2.424.40.4490.863194.1
2.42-2.484.40.3980.889195.1
2.48-2.554.40.3570.916195.4
2.55-2.624.40.2960.936194.7
2.62-2.714.40.2590.939196.3
2.71-2.814.40.2160.958196.2
2.81-2.924.40.1880.966196.8
2.92-3.054.30.1580.977197.6
3.05-3.214.30.1370.98198.7
3.21-3.414.30.1110.986199.1
3.41-3.684.30.0920.991199.4
3.68-4.054.40.0830.991199.3
4.05-4.634.40.0690.993199.3
4.63-5.834.50.0660.994198.9
5.83-504.10.0620.993195.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TE6

5te6


Resolution: 2.15→44.523 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.77
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 2023 3.83 %1
Rwork0.1898 ---
obs0.1912 52793 95.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 217.91 Å2 / Biso mean: 64.1265 Å2 / Biso min: 29.2 Å2
Refinement stepCycle: final / Resolution: 2.15→44.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 351 315 6642
Biso mean--106.29 49.29 -
Num. residues----771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036298
X-RAY DIFFRACTIONf_angle_d0.5398555
X-RAY DIFFRACTIONf_chiral_restr0.046965
X-RAY DIFFRACTIONf_plane_restr0.0031082
X-RAY DIFFRACTIONf_dihedral_angle_d10.2753752
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1497-2.20340.28331230.24943120324383
2.2034-2.2630.28391360.24553488362493
2.263-2.32960.2731430.23413548369195
2.3296-2.40480.25021430.23343520366395
2.4048-2.49070.27471410.22623548368995
2.4907-2.59040.26491550.23093570372595
2.5904-2.70830.25561320.21733581371395
2.7083-2.85110.26361510.22963647379896
2.8511-3.02960.2831440.21923665380997
3.0296-3.26350.25891440.20573738388299
3.2635-3.59180.20311460.18933766391299
3.5918-4.11120.20191550.17443824397999
4.1112-5.17850.16611530.14293844399799
5.1785-44.53240.24571570.18173911406896
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)
18.50320.62635.31632.73341.27666.09380.268-0.5445-0.65810.5752-0.08280.03560.6166-0.2505-0.15530.5421-0.06590.09650.32530.03470.3158-10.05298.038-26.9899
27.87455.18341.8737.38094.85253.5774-0.23260.808-0.1379-0.38420.148-0.1089-0.3655-0.13070.02680.29280.01650.05450.3893-0.05260.3151-11.47516.601-36.8466
37.64880.873.06123.5321-1.83367.794-0.1599-0.39350.08380.4062-0.02220.1696-0.0113-0.39940.15280.4558-0.00970.10880.3447-0.0860.3303-11.540116.9775-22.8799
46.47950.13633.95322.00720.11857.7093-0.17040.0698-0.04110.6627-0.11360.2989-0.2088-0.47060.27650.434-0.09480.08930.2732-0.02620.3784-15.806214.5462-33.3157
51.17570.6280.65251.48630.68511.08590.0409-0.0248-0.09620.0443-0.07110.2162-0.0208-0.07540.03870.2726-0.01420.0250.32780.03080.4201-18.79452.0102-49.7733
64.2743-0.5105-3.7206-0.13860.08647.2605-0.06120.2247-0.33-0.1970.04370.03770.4341-0.01360.09970.24940.0163-0.04780.3019-0.0260.4661-20.7638-8.7798-64.5
74.08460.1133-3.07963.44224.53124.8028-0.29920.1458-0.26990.02310.1340.3780.49170.11920.17770.3772-0.0363-0.01810.27520.00180.5156-27.488-10.4973-55.0406
81.17780.1262-0.10846.05864.08858.8447-0.01640.03080.1281-0.28030.0528-0.051-0.80840.0596-0.05050.2674-0.0690.00190.3270.02880.49541.390922.1165-47.7799
98.7535-1.9241-2.9161.9835-0.6226.7484-0.3134-0.5206-0.92010.32880.0119-0.16950.75970.38670.2320.3702-0.0114-0.01230.27940.08860.34875.863612.4015-40.9715
102.5713-1.7859-2.59638.77986.36838.7304-0.16950.0403-0.1470.04680.0305-0.0225-0.08090.11780.12270.2679-0.0286-0.07250.29730.05060.34833.064719.0262-46.2689
118.52445.10896.71566.60535.63895.7423-0.10380.518-0.1603-0.19350.5577-0.2031-0.49690.7628-0.34710.2617-0.04620.06460.318-0.02870.4639-3.88519.3344-64.1075
122.8136-1.29-1.83743.37341.04578.8286-0.1723-0.7943-0.9524-0.2248-0.02110.51670.7765-0.35990.17710.3329-0.0233-0.07130.2810.02090.558-32.3379-1.0972-64.8938
136.7351-1.07760.44471.4793-0.27292.32310.1191-0.0618-0.0042-0.1738-0.0566-0.0563-0.13710.2172-0.04950.2895-0.04980.0070.2475-0.04770.4227-19.56868.6578-64.5713
147.41141.3837-2.19162.824-1.87734.53490.00880.4498-0.3438-0.2618-0.06870.28230.0858-0.26350.04050.34660.0149-0.03990.2301-0.06890.463-29.72767.4418-71.0698
156.2190.2091-2.44053.31671.52347.23730.3771-0.07460.08270.3192-0.2114-0.8932-0.9943-0.0537-0.12930.7877-0.0588-0.02630.6693-0.01560.548717.347528.0987-0.0958
163.84752.6106-0.22944.604-0.46641.5450.0374-0.24080.04820.2047-0.0336-0.2464-0.0932-0.0061-0.03590.68960.0622-0.00580.5959-0.05090.424911.239126.6865-5.2148
175.2603-2.53093.19697.7403-3.27112.70210.02230.51691.1942-0.3165-0.4492-0.3847-0.25670.58950.27730.7673-0.0252-0.01260.76540.06560.674117.909538.6304-13.1064
187.65335.74023.72855.59182.70935.24260.4291-0.12530.7690.078-0.0981-0.0833-0.82660.8795-0.31750.70640.0770.01830.4345-0.03920.475112.176537.7-10.8437
191.85391.48570.68625.75723.98522.88220.0335-0.05390.36330.1925-0.0965-0.1658-0.50640.15980.03310.78420.0091-0.03850.4326-0.12080.52590.999938.064-17.2612
201.36530.8932-0.21674.5172-2.11184.74920.0066-0.45510.5540.4990.00830.3838-0.6662-0.1674-0.07240.62450.05080.04810.5314-0.20090.577-9.58835.7314-7.7251
211.04930.2614-0.0891.8589-1.12351.35520.1026-0.27110.24320.3067-0.09210.3432-0.0812-0.0517-0.0030.6558-0.01230.040.5157-0.15090.4729-5.474230.2087-8.9614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 33 )H1 - 33
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 45 )H34 - 45
3X-RAY DIFFRACTION3chain 'H' and (resid 46 through 82 )H46 - 82
4X-RAY DIFFRACTION4chain 'H' and (resid 82A through 95 )H82
5X-RAY DIFFRACTION5chain 'H' and (resid 96 through 175 )H96 - 175
6X-RAY DIFFRACTION6chain 'H' and (resid 176 through 194 )H176 - 194
7X-RAY DIFFRACTION7chain 'H' and (resid 195 through 216 )H195 - 216
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 38 )L1 - 38
9X-RAY DIFFRACTION9chain 'L' and (resid 39 through 61 )L39 - 61
10X-RAY DIFFRACTION10chain 'L' and (resid 62 through 102 )L62 - 102
11X-RAY DIFFRACTION11chain 'L' and (resid 103 through 113 )L103 - 113
12X-RAY DIFFRACTION12chain 'L' and (resid 114 through 128 )L114 - 128
13X-RAY DIFFRACTION13chain 'L' and (resid 129 through 174 )L129 - 174
14X-RAY DIFFRACTION14chain 'L' and (resid 175 through 214 )L175 - 214
15X-RAY DIFFRACTION15chain 'G' and (resid 45 through 73 )G45 - 73
16X-RAY DIFFRACTION16chain 'G' and (resid 74 through 215 )G74 - 215
17X-RAY DIFFRACTION17chain 'G' and (resid 216 through 235 )G216 - 235
18X-RAY DIFFRACTION18chain 'G' and (resid 236 through 258 )G236 - 258
19X-RAY DIFFRACTION19chain 'G' and (resid 259 through 283 )G259 - 283
20X-RAY DIFFRACTION20chain 'G' and (resid 284 through 385 )G284 - 385
21X-RAY DIFFRACTION21chain 'G' and (resid 386 through 491 )G386 - 491

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