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- PDB-3se9: Crystal structure of broadly and potently neutralizing antibody V... -

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Basic information

Entry
Database: PDB / ID: 3se9
TitleCrystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with HIV-1 gp120
Components
  • HIV-1 Clade AE strain 93TH057 gp120
  • Heavy chain of antibody VRC-PG04
  • Light chain of antibody VRC-PG04
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / GP120 / ANTIBODY / VRC-PG04 / NEUTRALIZATION / VACCINE / ENVELOPE GLYCOPROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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
(R,R)-2,3-BUTANEDIOL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKwong, P.D. / Zhou, T.
CitationJournal: Science / Year: 2011
Title: Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing.
Authors: Wu, X. / Zhou, T. / Zhu, J. / Zhang, B. / Georgiev, I. / Wang, C. / Chen, X. / Longo, N.S. / Louder, M. / McKee, K. / O'Dell, S. / Perfetto, S. / Schmidt, S.D. / Shi, W. / Wu, L. / Yang, Y. ...Authors: Wu, X. / Zhou, T. / Zhu, J. / Zhang, B. / Georgiev, I. / Wang, C. / Chen, X. / Longo, N.S. / Louder, M. / McKee, K. / O'Dell, S. / Perfetto, S. / Schmidt, S.D. / Shi, W. / Wu, L. / Yang, Y. / Yang, Z.Y. / Yang, Z. / Zhang, Z. / Bonsignori, M. / Crump, J.A. / Kapiga, S.H. / Sam, N.E. / Haynes, B.F. / Simek, M. / Burton, D.R. / Koff, W.C. / Doria-Rose, N.A. / Connors, M. / Mullikin, J.C. / Nabel, G.J. / Roederer, M. / Shapiro, L. / Kwong, P.D. / Mascola, J.R.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Jul 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_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Apr 7, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: HIV-1 Clade AE strain 93TH057 gp120
H: Heavy chain of antibody VRC-PG04
L: Light chain of antibody VRC-PG04
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,84142
Polymers86,9303
Non-polymers3,91139
Water9,998555
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.804, 66.476, 237.305
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 VRC-PG04


Mass: 24644.771 Da / Num. of mol.: 1 / Fragment: Antigen binding fragement of heavy chain
Source method: isolated from a genetically manipulated source
Details: Co-transfection of both heavy and light chain plasmids
Source: (gene. exp.) Homo sapiens (human) / Gene: antibody VRC-PG04 heavy chain / Plasmid: CMVR derived plasmids for IgG1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody Light chain of antibody VRC-PG04


Mass: 23073.822 Da / Num. of mol.: 1 / Fragment: antibody light chain
Source method: isolated from a genetically manipulated source
Details: Co-transfection of both heavy and light chain plasmids
Source: (gene. exp.) Homo sapiens (human) / Gene: antibody VRC-PG04 light chain / Plasmid: CMVR derived plasmids for IgG1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 11 molecules G

#1: Protein HIV-1 Clade AE strain 93TH057 gp120


Mass: 39211.434 Da / Num. of mol.: 1 / Fragment: Core gp120 with trancations
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: 93TH057 / Gene: gp120 / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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 , 6 types, 584 molecules

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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 9.9% PEG 4000, 9.0 % isopropanol, 100 mM Li2SO4, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 67230 / Num. obs: 59364 / % possible obs: 88.3 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_755)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→23.734 Å / SU ML: 0.51 / σ(F): 1.93 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 3002 5.07 %RANDOM
Rwork0.19 ---
obs0.1922 59260 88.31 %-
all-67229 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.269 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4438 Å2-0 Å2-0 Å2
2---1.1089 Å2-0 Å2
3----3.3349 Å2
Refinement stepCycle: LAST / Resolution: 2→23.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6027 0 221 555 6803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056378
X-RAY DIFFRACTIONf_angle_d0.9178641
X-RAY DIFFRACTIONf_dihedral_angle_d13.5632339
X-RAY DIFFRACTIONf_chiral_restr0.057976
X-RAY DIFFRACTIONf_plane_restr0.0041087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.03260.30471050.25541758X-RAY DIFFRACTION60
2.0326-2.06770.31221190.23991986X-RAY DIFFRACTION66
2.0677-2.10520.32621170.22972119X-RAY DIFFRACTION72
2.1052-2.14570.24861080.21832288X-RAY DIFFRACTION76
2.1457-2.18950.27911190.22752407X-RAY DIFFRACTION80
2.1895-2.2370.28431140.21882505X-RAY DIFFRACTION83
2.237-2.2890.26771600.21292624X-RAY DIFFRACTION87
2.289-2.34620.27331350.21862716X-RAY DIFFRACTION91
2.3462-2.40960.29381220.21862775X-RAY DIFFRACTION92
2.4096-2.48040.24251460.21362777X-RAY DIFFRACTION92
2.4804-2.56040.27631520.21742772X-RAY DIFFRACTION92
2.5604-2.65180.27951520.21252794X-RAY DIFFRACTION93
2.6518-2.75780.27761530.20832802X-RAY DIFFRACTION93
2.7578-2.88310.28021350.20642798X-RAY DIFFRACTION93
2.8831-3.03490.26111350.19922850X-RAY DIFFRACTION93
3.0349-3.22460.23181740.19272814X-RAY DIFFRACTION94
3.2246-3.47280.21711620.18482965X-RAY DIFFRACTION97
3.4728-3.8210.20591550.17493046X-RAY DIFFRACTION100
3.821-4.37090.19081710.1483092X-RAY DIFFRACTION100
4.3709-5.49560.18561860.14933106X-RAY DIFFRACTION100
5.4956-23.73530.22931820.20433264X-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)
12.16940.6502-0.75611.4552-0.16621.9443-0.0287-0.1204-0.10610.0436-0.060.14750.1805-0.24360.08790.4984-0.0196-0.03440.1737-0.02150.1455-12.87422.8996-50.9051
21.90910.5699-0.70481.231-0.50292.65440.00950.06780.1880.0059-0.00640.3489-0.3306-0.5256-0.0280.40470.0958-0.06150.2227-0.02460.2059-16.915825.3885-49.2023
30.93690.32650.39230.6220.54972.1919-0.03380.06390.02120.2688-0.0521-0.1201-0.10040.21380.03040.5657-0.0049-0.02930.17540.00880.12274.021128.6756-30.6826
44.1362-0.19710.51931.99330.56771.3155-0.095-0.1128-0.02590.09860.1125-0.1849-0.24040.2545-0.04750.6586-0.0744-0.0310.2047-0.02520.189224.833241.7962-3.2749
50.26760.1886-0.00040.4058-0.030.58310.1647-0.2222-0.13840.3895-0.1439-0.17720.0393-0.0011-0.09440.6646-0.097-0.14780.14090.1051-0.01750.094715.9171-11.6141
61.9931-0.05560.11672.0397-0.15931.89190.0253-0.33650.17420.30910.0450.1164-0.2514-0.077-0.07090.64090.0063-0.00110.2703-0.00480.19112.951743.43426.9627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain G and (resid 44:253 or resid 476:492)
2X-RAY DIFFRACTION2chain G and resid 254:475
3X-RAY DIFFRACTION3chain H and resid 1:114
4X-RAY DIFFRACTION4chain H and resid 115:216
5X-RAY DIFFRACTION5chain L and resid 1:111
6X-RAY DIFFRACTION6chain L and resid 112:213

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