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- PDB-2ny7: HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neut... -

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Basic information

Entry
Database: PDB / ID: 2ny7
TitleHIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12
Components
  • ANTIBODY b12, HEAVY CHAIN
  • ANTIBODY b12, LIGHT CHAIN
  • ENVELOPE GLYCOPROTEIN GP120
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / gp120 / broadly neutralizing antibody / b12 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Synthesis and processing of ENV and VPU / evasion of host immune response / CD22 mediated BCR regulation / Alpha-defensins / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Synthesis and processing of ENV and VPU / evasion of host immune response / CD22 mediated BCR regulation / Alpha-defensins / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / Dectin-2 family / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Binding and entry of HIV virion / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / antigen binding / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / host cell endosome membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Assembly Of The HIV Virion / Budding and maturation of HIV virion / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / clathrin-dependent endocytosis of virus by host cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / viral protein processing / immune response / symbiont entry into host cell / 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 / extracellular space / extracellular exosome / extracellular region / 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 / Immunoglobulin/major histocompatibility complex, conserved site ...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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhou, T. / Xu, L. / Dey, B. / Hessell, A.J. / Van Ryk, D. / Xiang, S.H. / Yang, X. / Zhang, M.Y. / Zwick, M.B. / Arthos, J. ...Zhou, T. / Xu, L. / Dey, B. / Hessell, A.J. / Van Ryk, D. / Xiang, S.H. / Yang, X. / Zhang, M.Y. / Zwick, M.B. / Arthos, J. / Burton, D.R. / Dimitrov, D.S. / Sodroski, J. / Wyatt, R. / Nabel, G.J. / Kwong, P.D.
CitationJournal: Nature / Year: 2007
Title: Structural definition of a conserved neutralization epitope on HIV-1 gp120.
Authors: Zhou, T. / Xu, L. / Dey, B. / Hessell, A.J. / Van Ryk, D. / Xiang, S.H. / Yang, X. / Zhang, M.Y. / Zwick, M.B. / Arthos, J. / Burton, D.R. / Dimitrov, D.S. / Sodroski, J. / Wyatt, R. / Nabel, G.J. / Kwong, P.D.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jul 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 30, 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

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Assembly

Deposited unit
G: ENVELOPE GLYCOPROTEIN GP120
H: ANTIBODY b12, HEAVY CHAIN
L: ANTIBODY b12, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,62116
Polymers83,7453
Non-polymers2,87613
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint13 kcal/mol
Surface area35060 Å2
MethodPISA
2
G: ENVELOPE GLYCOPROTEIN GP120
H: ANTIBODY b12, HEAVY CHAIN
L: ANTIBODY b12, LIGHT CHAIN
hetero molecules

G: ENVELOPE GLYCOPROTEIN GP120
H: ANTIBODY b12, HEAVY CHAIN
L: ANTIBODY b12, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,24232
Polymers167,4906
Non-polymers5,75126
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_576x,x-y+2,-z+11/61
Buried area19410 Å2
ΔGint31 kcal/mol
Surface area69180 Å2
MethodPISA
3
G: ENVELOPE GLYCOPROTEIN GP120
hetero molecules

G: ENVELOPE GLYCOPROTEIN GP120
hetero molecules

H: ANTIBODY b12, HEAVY CHAIN
L: ANTIBODY b12, LIGHT CHAIN

H: ANTIBODY b12, HEAVY CHAIN
L: ANTIBODY b12, LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)173,24232
Polymers167,4906
Non-polymers5,75126
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+11/61
crystal symmetry operation5_575y,-x+y+2,z+1/61
crystal symmetry operation7_546y,x-1,-z+5/31
Buried area16720 Å2
ΔGint16 kcal/mol
Surface area71870 Å2
MethodPISA
4
G: ENVELOPE GLYCOPROTEIN GP120
hetero molecules

G: ENVELOPE GLYCOPROTEIN GP120
hetero molecules

H: ANTIBODY b12, HEAVY CHAIN
L: ANTIBODY b12, LIGHT CHAIN

H: ANTIBODY b12, HEAVY CHAIN
L: ANTIBODY b12, LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)173,24232
Polymers167,4906
Non-polymers5,75126
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+11/61
crystal symmetry operation5_565y,-x+y+1,z+1/61
crystal symmetry operation7_556y,x,-z+5/31
Buried area17620 Å2
ΔGint22 kcal/mol
Surface area70970 Å2
MethodPISA
5
G: ENVELOPE GLYCOPROTEIN GP120
H: ANTIBODY b12, HEAVY CHAIN
L: ANTIBODY b12, LIGHT CHAIN
hetero molecules

G: ENVELOPE GLYCOPROTEIN GP120
H: ANTIBODY b12, HEAVY CHAIN
L: ANTIBODY b12, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,24232
Polymers167,4906
Non-polymers5,75126
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+11/61
Buried area21280 Å2
ΔGint18 kcal/mol
Surface area67300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.955, 101.955, 298.294
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ENVELOPE GLYCOPROTEIN GP120 /


Mass: 35126.867 Da / Num. of mol.: 1 / Fragment: CORE
Mutation: M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: HXBc2 / Plasmid: CMVR / Cell line (production host): embryonic cell line 293 / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: P04578
#2: Antibody ANTIBODY b12, HEAVY CHAIN


Mass: 24910.846 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1
#3: Antibody ANTIBODY b12, LIGHT CHAIN


Mass: 23707.354 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1 / References: UniProt: P01834*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.: 13 / Source method: obtained synthetically / 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.: 308 / 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: 2.67 Å3/Da / Density % sol: 53.95 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 41973 / Num. obs: 40798 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.382.30.755177.5
2.38-2.484.30.772196
2.48-2.597.50.694199.7
2.59-2.7310.10.5231100
2.73-2.910.90.3561100
2.9-3.1210.90.2271100
3.12-3.4410.70.1491100
3.44-3.9310.30.1041100
3.93-4.959.70.079199.7
4.95-509.70.057198.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1HZH, 1GC1

1hzh

1gc1


Resolution: 2.3→49.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 15.885 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Authors state that because crystals were small and subject to high radiation dosages during data collection, difference fouriers comparing the initial and final swatches of data were ...Details: Authors state that because crystals were small and subject to high radiation dosages during data collection, difference fouriers comparing the initial and final swatches of data were inspected to identify radiation-induced disulfide breakage, and the refined models were adjusted to reflect the initial, radiation-damage free structure. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25503 1890 5 %RANDOM
Rwork0.19291 ---
obs0.19601 36114 93.26 %-
all-40751 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 182 308 6177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0226031
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8521.9728204
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.185730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.69124.087252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65715952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8291532
X-RAY DIFFRACTIONr_chiral_restr0.0560.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024485
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.32484
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.54103
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.5538
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.355
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1741.53717
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.23525922
X-RAY DIFFRACTIONr_scbond_it5.29632595
X-RAY DIFFRACTIONr_scangle_it7.2814.52282
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 93 -
Rwork0.254 1693 -
obs--80.31 %
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)
17.2095-2.8599-0.001416.2817-4.51296.27780.5191-0.09811.47940.1938-0.3675-2.3517-0.8546-0.1864-0.15160.076-0.1584-0.29360.04660.07870.9616115.1153156.7278271.1539
25.7271-0.78530.00225.8699-0.35052.8943-0.0348-0.54280.70450.9793-0.0517-0.5819-0.1437-0.04370.08650.025-0.0594-0.2434-0.2029-0.089-0.061198.3635147.7646278.3407
30.84070.11530.38192.12251.23865.81920.04480.14390.089-0.07950.0493-0.50560.02220.3291-0.0941-0.28320.01940.0038-0.24540.0539-0.1699.1587132.6909252.2531
48.2352.9976-1.02354.3679-1.05522.8255-0.35860.7686-0.5337-1.05010.3672-0.20040.3286-0.3679-0.00860.1069-0.06310.1126-0.115-0.0877-0.283579.0099123.2715221.9189
52.37281.37660.79753.69060.93154.16530.1170.068-0.17160.1877-0.0536-0.09110.6556-0.0179-0.0634-0.09140.0209-0.0197-0.3070.0506-0.302988.1068114.5802257.3391
64.0511.8023-3.26035.8889-0.67739.5326-0.32580.4531-0.7371-1.26920.214-1.14910.58140.16630.11180.182-0.04870.2634-0.1634-0.22190.135983.8545108.3587222.3273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1GA83 - 2551 - 109
2X-RAY DIFFRACTION1GD - E734 - 741
3X-RAY DIFFRACTION2GA256 - 492110 - 317
4X-RAY DIFFRACTION2GF - P762 - 963
5X-RAY DIFFRACTION3HB1 - 1271 - 141
6X-RAY DIFFRACTION4HB128 - 230142 - 230
7X-RAY DIFFRACTION5LC1 - 1101 - 111
8X-RAY DIFFRACTION6LC111 - 214112 - 215

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