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- PDB-4i3s: Crystal structure of the outer domain of HIV-1 gp120 in complex w... -

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Basic information

Entry
Database: PDB / ID: 4i3s
TitleCrystal structure of the outer domain of HIV-1 gp120 in complex with VRC-PG04 space group P21
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 / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / 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: 2.85 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 1.3May 26, 2021Group: Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn ...entity_src_gen / struct_conn / struct_conn_type / struct_site
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 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
Revision 1.5Dec 27, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)68,5334
Polymers68,4933
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.647, 73.471, 109.292
Angle α, β, γ (deg.)90.00, 100.94, 90.00
Int Tables number4
Space group name H-MP1211
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 52.5% peg 400, 100 mM HEPES pH7.5, 200 mM CaCl2, 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 26, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 14947 / % possible obs: 85.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 47.83 Å2 / Rmerge(I) obs: 0.225 / Rsym value: 0.225 / Net I/σ(I): 6.21
Reflection shellResolution: 2.85→2.93 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.01 / Rsym value: 0.9 / % possible all: 76.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SE9

3se9


Resolution: 2.85→46.78 Å / Cor.coef. Fo:Fc: 0.8262 / Cor.coef. Fo:Fc free: 0.7166 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3199 1075 7.19 %RANDOM
Rwork0.2483 ---
obs0.2534 14941 85.41 %-
all-17504 --
Displacement parametersBiso mean: 41.38 Å2
Baniso -1Baniso -2Baniso -3
1-6.9102 Å20 Å21.8997 Å2
2---6.0238 Å20 Å2
3----0.8864 Å2
Refine analyzeLuzzati coordinate error obs: 0.508 Å
Refinement stepCycle: LAST / Resolution: 2.85→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4689 0 1 0 4690
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094801HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.196518HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1629SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes700HARMONIC5
X-RAY DIFFRACTIONt_it4801HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion22.68
X-RAY DIFFRACTIONt_chiral_improper_torsion639SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4978SEMIHARMONIC4
LS refinement shellResolution: 2.85→3.05 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.311 180 7.49 %
Rwork0.2345 2224 -
all0.2405 2404 -
obs--85.41 %
Refinement TLS params.Method: refined / Origin x: 7.0622 Å / Origin y: -16.8376 Å / Origin z: 23.6352 Å
111213212223313233
T-0.1664 Å2-0.0586 Å20.1713 Å2--0.3713 Å2-0.0357 Å2--0.0587 Å2
L1.6014 °2-0.6235 °2-1.029 °2-0.9787 °20.3716 °2--0.9498 °2
S-0.0231 Å °0.1198 Å °-0.1797 Å °-0.0352 Å °-0.0144 Å °0.1216 Å °-0.0373 Å °0.0454 Å °0.0375 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }G252 - 477
2X-RAY DIFFRACTION1{ *|* }H1 - 215
3X-RAY DIFFRACTION1{ *|* }L1 - 214
4X-RAY DIFFRACTION1{ *|* }L301

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