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- PDB-4i3r: Crystal structure of the outer domain of HIV-1 gp120 in complex w... -

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Basic information

Entry
Database: PDB / ID: 4i3r
TitleCrystal structure of the outer domain of HIV-1 gp120 in complex with VRC-PG04 space group P3221
Components
  • Heavy chain of VRC-PG04 Fab
  • Light chain of VRC-PG04 Fab
  • Outer domain of HIV-1 gp120 (KER2018 OD4.2.2)
KeywordsViral Protein/Immune System / Antibody Affinity / Antibody Specificity / Binding Sites / HIV Infections / Antibodies / HIV Envelope Protein gp120 / AIDS Vaccines / Amino Acid Sequence / Antigens / Epitopes / HIV Antibodies / CD4 / Somatic Mutation / Sequence engineering / Complementarity Determining Regions / Immunoglobulin Fab Fragments / Sera / 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
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / Resolution: 3 Å
AuthorsJoyce, M.G. / Biertumpfel, C. / Nabel, G.J. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2013
Title: Outer Domain of HIV-1 gp120: Antigenic Optimization, Structural Malleability, and Crystal Structure with Antibody VRC-PG04.
Authors: Joyce, M.G. / Kanekiyo, M. / Xu, L. / Biertumpfel, C. / Boyington, J.C. / Moquin, S. / Shi, W. / Wu, X. / Yang, Y. / Yang, Z.Y. / Zhang, B. / Zheng, A. / Zhou, T. / Zhu, J. / Mascola, J.R. / ...Authors: Joyce, M.G. / Kanekiyo, M. / Xu, L. / Biertumpfel, C. / Boyington, J.C. / Moquin, S. / Shi, W. / Wu, X. / Yang, Y. / Yang, Z.Y. / Zhang, B. / Zheng, A. / Zhou, T. / Zhu, J. / Mascola, J.R. / Kwong, P.D. / Nabel, G.J.
History
DepositionNov 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Jul 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 1.4May 26, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Outer domain of HIV-1 gp120 (KER2018 OD4.2.2)
H: Heavy chain of VRC-PG04 Fab
L: Light chain of VRC-PG04 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3787
Polymers68,4933
Non-polymers8854
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-16 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.910, 158.910, 80.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe Biological unit is identical to that found in the asymmetric unit.

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Components

#1: Protein Outer domain of HIV-1 gp120 (KER2018 OD4.2.2)


Mass: 20774.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human Immunodeficiency Virus / Cell line (production host): 293S / Production host: Homo sapiens (human) / References: UniProt: Q3ZLH8*PLUS
#2: Antibody Heavy chain of VRC-PG04 Fab


Mass: 24644.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody Light chain of VRC-PG04 Fab


Mass: 23073.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.27 Å3/Da / Density % sol: 71.2 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 10% peg400, 20% peg8000, 100 mM Na-acetate pH5.5, 500 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 22975 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 21.82
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.61 / % possible all: 88.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SE9

3se9


Resolution: 3→43.65 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 26.67 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.245 1380 6.01 %
Rwork0.183 --
obs0.186 22971 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4806 0 53 4 4863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094994
X-RAY DIFFRACTIONf_angle_d1.2996774
X-RAY DIFFRACTIONf_dihedral_angle_d17.3391816
X-RAY DIFFRACTIONf_chiral_restr0.083763
X-RAY DIFFRACTIONf_plane_restr0.005871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.001-3.10820.35641310.30991985X-RAY DIFFRACTION91
3.1082-3.23270.39981580.29582143X-RAY DIFFRACTION98
3.2327-3.37970.30851410.26042162X-RAY DIFFRACTION99
3.3797-3.55780.31871350.22732157X-RAY DIFFRACTION99
3.5578-3.78060.28651460.19862188X-RAY DIFFRACTION99
3.7806-4.07230.23931340.1752151X-RAY DIFFRACTION98
4.0723-4.48180.17841320.13892178X-RAY DIFFRACTION98
4.4818-5.12940.1871580.13062175X-RAY DIFFRACTION98
5.1294-6.45920.20761320.17242189X-RAY DIFFRACTION98
6.4592-43.65640.25981130.17932263X-RAY DIFFRACTION96
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)
12.05031.9634.95532.02834.8252.09790.406-1.1721-0.74842.13640.43711.08454.0807-1.3793-0.71591.3534-0.3162-0.26170.90150.36791.131159.6013-36.2938-5.3695
21.5122-0.2754-0.32987.8521-1.49772.53260.25750.0816-0.4949-1.02730.08650.38070.8403-0.1249-0.35821.2051-0.1047-0.28130.49110.02410.643361.9825-38.9028-22.4094
33.58740.6104-0.33860.1368-0.60374.7013-0.91860.2872-1.21230.369-0.6606-0.07141.52621.34241.20782.10350.06250.6961.5575-0.4551.565671.5015-40.225-37.7009
48.6899-1.7955-0.32372.1521-4.30019.1584-0.47090.0439-0.758-1.17510.5278-0.01150.20520.6182-0.39181.7849-0.1328-0.37140.5416-0.04860.894670.8701-49.278-17.1153
57.52283.39996.11641.52412.70934.91441.2067-0.541-0.67912.64080.68-2.1366-0.0453-0.0657-1.69142.3569-0.0776-0.35431.15140.29781.490369.3692-60.0448-2.931
64.0619-6.21651.97967.1883-5.04094.7952-0.05660.18530.1751-1.10930.56960.50350.3705-0.5336-0.48630.8867-0.026-0.18770.4469-0.03410.420263.7623-35.4022-21.7967
71.9134-9.35172.73869.35950.88922.02131.17842.0863-1.0173-1.0515-0.24164.08330.5988-1.2323-0.84041.2738-0.1696-0.35041.30380.18711.45651.1789-31.4962-11.4577
85.01982.54916.71574.82071.10672.1040.717-2.21923.76171.5796-0.8827-0.704-1.44730.40140.06961.8532-0.4754-0.16030.8566-0.15341.042171.6704-12.65344.2473
92.39412.78841.25925.84251.49762.69080.4912-0.3619-0.5381.037-0.205-0.92450.10470.305-0.28170.8042-0.1531-0.20160.4880.15230.684874.777-15.9269-6.2527
10-0.0003-0.0033-0.0052-0.03420.01310.0007-1.5586-0.0722-0.2801-2.55740.22-2.4025-0.1355-1.21930.83113.4149-0.1950.02161.20710.01871.218393.018329.6381-4.3366
115.745-0.66431.84913.43136.6886.73370.1137-0.5066-0.43770.91140.1736-1.08190.09910.6552-0.32261.0861-0.3577-0.2870.79980.19270.985392.169211.76972.3806
125.1241-0.4121.77786.4003-0.69395.51370.0666-0.22540.66770.5536-0.20260.4944-0.5237-0.06710.13660.7519-0.10850.09750.37910.06390.565660.17230.2492-12.1805
138.3423-2.3955-0.55444.62440.27022.0360.15690.37180.3209-0.3643-0.1072-0.9651-0.52440.737-0.07271.0597-0.35070.04590.78020.030.774391.117718.2558-13.0073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain G and resid 252:257)
2X-RAY DIFFRACTION2(chain G and resid 258:396)
3X-RAY DIFFRACTION3(chain G and resid 397:412)
4X-RAY DIFFRACTION4(chain G and resid 413:421)
5X-RAY DIFFRACTION5(chain G and resid 422:441)
6X-RAY DIFFRACTION6(chain G and resid 442:470)
7X-RAY DIFFRACTION7(chain G and resid 471:484)
8X-RAY DIFFRACTION8(chain H and resid 1:9)
9X-RAY DIFFRACTION9(chain H and resid 10:126)
10X-RAY DIFFRACTION10(chain H and resid 127:134)
11X-RAY DIFFRACTION11(chain H and resid 135:215)
12X-RAY DIFFRACTION12(chain L and resid 1:104)
13X-RAY DIFFRACTION13(chain L and resid 105:214)

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