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- PDB-3jwd: Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Ar... -

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Basic information

Entry
Database: PDB / ID: 3jwd
TitleStructure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility
Components
  • FAB 48D HEAVY CHAIN
  • FAB 48D LIGHT CHAIN
  • HIV-1 GP120 ENVELOPE GLYCOPROTEIN
  • T-cell surface glycoprotein CD4
KeywordsVIRAL PROTEIN / HIV-1 VIRAL SPIKE / MOLECULAR MOTION / PROTEIN ARCHITECTURE / RECEPTOR-TRIGGERED ENTRY / TYPE 1 FUSION PROTEIN / CELL MEMBRANE / DISULFIDE BOND / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE
Function / homology
Function and homology information


helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / positive regulation of interleukin-2 production / T cell activation / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of T cell activation / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / virus receptor activity / signaling receptor activity / Clathrin-mediated endocytosis / MHC class II protein complex binding / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / early endosome / cell adhesion / immune response / positive regulation of protein phosphorylation / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / lipid binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Immunoglobulin ...CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Immunoglobulin / Immunoglobulin domain / Beta Complex / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD4
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsPancera, M. / Majeed, S. / Ban, Y.A. / Chen, L. / Huang, C.C. / Kong, L. / Kwon, Y.D. / Stuckey, J. / Zhou, T. / Robinson, J.E. ...Pancera, M. / Majeed, S. / Ban, Y.A. / Chen, L. / Huang, C.C. / Kong, L. / Kwon, Y.D. / Stuckey, J. / Zhou, T. / Robinson, J.E. / Schief, W.R. / Sodroski, J. / Wyatt, R. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility.
Authors: Pancera, M. / Majeed, S. / Ban, Y.E. / Chen, L. / Huang, C.C. / Kong, L. / Kwon, Y.D. / Stuckey, J. / Zhou, T. / Robinson, J.E. / Schief, W.R. / Sodroski, J. / Wyatt, R. / Kwong, P.D.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif
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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: HIV-1 GP120 ENVELOPE GLYCOPROTEIN
C: T-cell surface glycoprotein CD4
L: FAB 48D LIGHT CHAIN
H: FAB 48D HEAVY CHAIN
B: HIV-1 GP120 ENVELOPE GLYCOPROTEIN
D: T-cell surface glycoprotein CD4
O: FAB 48D LIGHT CHAIN
P: FAB 48D HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,99729
Polymers218,6108
Non-polymers4,38721
Water8,107450
1
A: HIV-1 GP120 ENVELOPE GLYCOPROTEIN
C: T-cell surface glycoprotein CD4
L: FAB 48D LIGHT CHAIN
H: FAB 48D HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,51714
Polymers109,3054
Non-polymers2,21210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-3 kcal/mol
Surface area47140 Å2
MethodPISA
2
B: HIV-1 GP120 ENVELOPE GLYCOPROTEIN
D: T-cell surface glycoprotein CD4
O: FAB 48D LIGHT CHAIN
P: FAB 48D HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,48015
Polymers109,3054
Non-polymers2,17511
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-7 kcal/mol
Surface area45700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.112, 172.954, 193.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
13
23
33
14
24
34

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B AND (RESSEQ 36:74)
311CHAIN B AND (RESSEQ 84:124)
411CHAIN B AND (RESSEQ 198:299)
511CHAIN B AND (RESSEQ 329:394)
611CHAIN B AND (RESSEQ 411:494)
112CHAIN L
212CHAIN O AND (RESSEQ 2:121)
312CHAIN O AND (RESSEQ 129:210)
113CHAIN H
213CHAIN P AND (RESSEQ 1:122)
313CHAIN P AND (RESSEQ 134:213)
114CHAIN C
214CHAIN D AND (RESSEQ 1000:1056)
314CHAIN D AND (RESSEQ 1060:1179)

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein HIV-1 GP120 ENVELOPE GLYCOPROTEIN


Mass: 42117.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: HXBC2 / Plasmid: PMT / Production host: DROSOPHILA MELANOGASTER (fruit fly)
#2: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 20419.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01730

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Antibody , 2 types, 4 molecules LOHP

#3: Antibody FAB 48D LIGHT CHAIN


Mass: 23252.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell (production host): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
Production host: unidentified herpesvirus
#4: Antibody FAB 48D HEAVY CHAIN


Mass: 23515.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell (production host): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
Production host: unidentified herpesvirus

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Sugars , 1 types, 19 molecules

#5: 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.: 19
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 , 2 types, 452 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 293 K / pH: 9.5
Details: 4.5 % PEG 8000, 01M CHES, pH 9.50, 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
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 2, 2006
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 59657 / % possible obs: 69.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 56.15 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.077 / Net I/σ(I): 20.5
Reflection shellResolution: 2.61→2.7 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.38 / Rsym value: 0.475 / % possible all: 17.2

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Processing

Software
NameVersionClassification
AMoREphasing
PHENIX(CCI APPS 2007_04_06_1210)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1RZJ, 1RZ7

1rzj

1rz7


Resolution: 2.61→43.86 Å
Details: WHEN REFINING TLS, THE OUTPUT PDB FILE ALWAYS HAS THE ANISOU RECORDS FOR THE ATOMS INVOLVED IN TLS GROUPS. THE ANISOTROPIC B-FACTOR IN ANISOU RECORDS IS THE TOTAL B-FACTOR (B_TLS + B_ ...Details: WHEN REFINING TLS, THE OUTPUT PDB FILE ALWAYS HAS THE ANISOU RECORDS FOR THE ATOMS INVOLVED IN TLS GROUPS. THE ANISOTROPIC B-FACTOR IN ANISOU RECORDS IS THE TOTAL B-FACTOR (B_TLS + B_INDIVIDUAL). THE ISOTROPIC EQUIVALENT B-FACTOR IN ATOM RECORDS IS THE MEAN OF THE TRACE OF THE ANISOU MATRIX DIVIDED BY 10000 AND MULTIPLIED BY 8*PI^2 AND REPRESENTS THE ISOTROPIC EQUIVALENT OF THE TOTAL B-FACTOR (B_TLS + B_INDIVIDUAL). TO OBTAIN THE INDIVIDUAL B-FACTORS, ONE NEEDS TO COMPUTE THE TLS COMPONENT (B_TLS) USING THE TLS RECORDS IN THE PDB FILE HEADER AND THEN SUBTRACT IT FROM THE TOTAL B-FACTORS (ON THE ANISOU RECORDS).
RfactorNum. reflection% reflection
Rfree0.275 5512 10.13 %
Rwork0.201 --
obs-54419 63.8 %
Displacement parametersBiso mean: 114.42 Å2
Baniso -1Baniso -2Baniso -3
1-34.67 Å20 Å20 Å2
2---1.46 Å20 Å2
3----33.22 Å2
Refinement stepCycle: LAST / Resolution: 2.61→43.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14969 0 278 450 15697
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0
X-RAY DIFFRACTIONf_angle_d0.35
X-RAY DIFFRACTIONf_dihedral_angle_d8.1
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
13BX-RAY DIFFRACTIONPOSITIONAL
14BX-RAY DIFFRACTIONPOSITIONAL
15BX-RAY DIFFRACTIONPOSITIONAL
16BX-RAY DIFFRACTIONPOSITIONAL
21LX-RAY DIFFRACTIONPOSITIONAL
22OX-RAY DIFFRACTIONPOSITIONAL
23OX-RAY DIFFRACTIONPOSITIONAL
31HX-RAY DIFFRACTIONPOSITIONAL
32PX-RAY DIFFRACTIONPOSITIONAL
33PX-RAY DIFFRACTIONPOSITIONAL
41CX-RAY DIFFRACTIONPOSITIONAL
42DX-RAY DIFFRACTIONPOSITIONAL
43DX-RAY DIFFRACTIONPOSITIONAL
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)
10.40550.1046-0.54391.0227-0.18353.6650.0167-0.02140.04550.0982-0.05390.07780.3314-0.31620.02430.1665-0.037-0.03410.25360.02640.352918.387667.7836108.339
22.42041.4338-1.10811.4207-0.61451.66170.1995-0.3008-0.0527-0.0931-0.3524-0.0955-0.36980.10640.06180.4217-0.03910.1160.28240.03140.338323.481886.89886.907
3-0.35150.3888-1.34290.6795-0.35118.08070.31270.00840.10270.0903-0.16030.0459-1.5280.3615-0.14480.5755-0.12830.0970.51530.15470.451422.9129102.988557.1569
42.2579-0.8477-0.65861.3020.34191.2335-0.4689-0.3386-0.29390.52560.10390.00320.79850.04290.33810.7460.30330.14130.32060.05170.348242.789939.998473.569
5-0.0113-0.0725-0.29072.2082-0.24590.51290.34290.34630.28020.0598-0.4737-0.6025-0.16160.06440.08280.65470.16470.2950.67210.41770.761564.033647.735545.0083
61.0367-0.2372-1.93291.80740.53963.15540.52960.59750.1993-1.0437-0.311-0.3895-0.4041-0.8635-0.1790.86020.43480.25310.54730.21930.491233.658959.614466.4946
72.4653-1.5682-3.6443.0204-0.29194.50121.33671.42580.1532-1.3553-0.8512-0.0403-0.3325-2.0523-0.45931.72910.8780.23981.39010.21520.689449.667747.931438.6141
80.8082-1.0161-0.43981.14190.89924.0865-0.02530.113-0.0849-0.08820.1681-0.02750.38691.3077-0.14170.39270.2286-0.05210.85880.01730.580158.714968.3867160.0519
94.72130.09650.3650.86070.11717.75550.0321-0.2276-0.3911-0.0298-0.0382-0.0349-1.34022.292-0.01340.5764-0.19020.06451.11340.04920.411459.680988.6261181.0668
10-0.92621.0460.0977-0.39940.46399.91480.4737-0.14760.11680.34750.31970.0419-0.29610.2206-0.65770.8321-0.0301-0.01981.1634-0.19010.56764.3276103.7747211.0396
111.1883-1.0264-1.4582-3.24210.36262.2339-1.17460.3762-1.0183-0.05140.0549-0.39451.5448-0.37381.15191.7329-0.49820.4290.51120.09151.125524.659251.4166193.0082
120.86472.45660.01965.2244-2.18161.4442-0.0678-0.1321-0.0049-0.60470.49871.21850.4442-0.3901-0.42220.9539-0.0450.31220.88270.22861.7776.548766.3501220.8797
130.3535-0.6464-0.00671.2564-0.02252.7622-0.2561-0.0792-0.03110.89390.10780.33630.37230.62070.1160.70620.16140.17030.48690.16540.680140.046766.4144200.9097
140.832-0.3252-1.14890.18840.50710.8534-0.3012-0.19590.12190.15920.25550.53590.54610.03450.04021.36510.14540.67470.76190.47041.367519.906961.4106227.4791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 31:501A31 - 501
2X-RAY DIFFRACTION2chain C and resid 1000:1098C1000 - 1098
3X-RAY DIFFRACTION3chain C and resid 1099:1183C1099 - 1183
4X-RAY DIFFRACTION4chain L and resid 1:111L1 - 111
5X-RAY DIFFRACTION5chain L and resid 112:214L112 - 214
6X-RAY DIFFRACTION6chain H and resid 1:128H1 - 128
7X-RAY DIFFRACTION7chain H and resid 129:214H129 - 214
8X-RAY DIFFRACTION8chain B and resid 31:499B31 - 499
9X-RAY DIFFRACTION9chain D and resid 1001:1098D1001 - 1098
10X-RAY DIFFRACTION10chain D and resid 1099:1183D1099 - 1183
11X-RAY DIFFRACTION11chain O and resid 1:111O1 - 111
12X-RAY DIFFRACTION12chain O and resid 112:213O112 - 213
13X-RAY DIFFRACTION13chain P and resid 1:128P1 - 128
14X-RAY DIFFRACTION14chain P and resid 129:212P129 - 212

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