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- PDB-4ywg: Crystal structure of 830A in complex with V1V2 -

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Basic information

Entry
Database: PDB / ID: 4ywg
TitleCrystal structure of 830A in complex with V1V2
Components
  • Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A
  • Light chain of anti-HIV-1 gp120 V1V2 antibody 830A
  • Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109
KeywordsViral protein/Immune system / HIV-1 gp120 / the V1V2 Region / antibody / complex structure / 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
Ubiquitin-like (UB roll) - #10 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ubiquitin-like (UB roll) / Roll / Immunoglobulins ...Ubiquitin-like (UB roll) - #10 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ubiquitin-like (UB roll) / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha 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 / Resolution: 2.998 Å
AuthorsPan, R. / Kong, X.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI084119 United States
CitationJournal: J.Virol. / Year: 2015
Title: The V1V2 Region of HIV-1 gp120 Forms a Five-Stranded Beta Barrel.
Authors: Pan, R. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Jul 27, 2016Group: Data collection
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 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
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light chain of anti-HIV-1 gp120 V1V2 antibody 830A
H: Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A
G: Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109
M: Light chain of anti-HIV-1 gp120 V1V2 antibody 830A
I: Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A
Q: Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,99012
Polymers122,6626
Non-polymers1,3276
Water00
1
L: Light chain of anti-HIV-1 gp120 V1V2 antibody 830A
H: Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A
G: Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9956
Polymers61,3313
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-15 kcal/mol
Surface area27220 Å2
MethodPISA
2
M: Light chain of anti-HIV-1 gp120 V1V2 antibody 830A
I: Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A
Q: Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9956
Polymers61,3313
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-19 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.725, 159.168, 170.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Light chain of anti-HIV-1 gp120 V1V2 antibody 830A


Mass: 23692.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293S / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A


Mass: 23976.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293S / Production host: Homo sapiens (human)
#3: Protein Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109


Mass: 13662.056 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / References: UniProt: Q6TCP8*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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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
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: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16.5% polyethylene glycol 8000 and 0.1 M Tris pH 8.5
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.998→49.029 Å / Num. obs: 35990 / % possible obs: 99.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.16
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.26 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KDM

3kdm


Resolution: 2.998→49.029 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.296 1623 4.91 %
Rwork0.219 --
obs0.2228 35968 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.998→49.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8065 0 84 0 8149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098346
X-RAY DIFFRACTIONf_angle_d1.41711358
X-RAY DIFFRACTIONf_dihedral_angle_d17.7332934
X-RAY DIFFRACTIONf_chiral_restr0.0521321
X-RAY DIFFRACTIONf_plane_restr0.0071430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9983-3.04120.41631300.39672608X-RAY DIFFRACTION97
3.0412-3.08660.45181450.37922686X-RAY DIFFRACTION99
3.0866-3.13480.40841370.34462711X-RAY DIFFRACTION100
3.1348-3.18620.42611300.32922692X-RAY DIFFRACTION100
3.1862-3.24110.37971640.31812695X-RAY DIFFRACTION100
3.2411-3.30.36471270.30672678X-RAY DIFFRACTION100
3.3-3.36350.36141530.30042714X-RAY DIFFRACTION100
3.3635-3.43210.37921310.29212695X-RAY DIFFRACTION100
3.4321-3.50670.36421510.27382666X-RAY DIFFRACTION100
3.5067-3.58830.32721310.26082733X-RAY DIFFRACTION100
3.5883-3.6780.3661440.24882631X-RAY DIFFRACTION100
3.678-3.77740.31371410.22942723X-RAY DIFFRACTION100
3.7774-3.88850.27141280.2382718X-RAY DIFFRACTION100
3.8885-4.01390.27821610.22282675X-RAY DIFFRACTION100
4.0139-4.15730.26691360.21212689X-RAY DIFFRACTION100
4.1573-4.32370.24991310.19272739X-RAY DIFFRACTION100
4.3237-4.52030.27031540.18762651X-RAY DIFFRACTION100
4.5203-4.75850.28281190.19092719X-RAY DIFFRACTION100
4.7585-5.05630.28371290.19122697X-RAY DIFFRACTION99
5.0563-5.44630.3161460.19532669X-RAY DIFFRACTION99
5.4463-5.99350.27571320.20762675X-RAY DIFFRACTION99
5.9935-6.85870.31441480.21442684X-RAY DIFFRACTION99
6.8587-8.63360.26191240.19682685X-RAY DIFFRACTION99
8.6336-49.03550.25191330.18332543X-RAY DIFFRACTION94

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