[English] 日本語
Yorodumi
- PDB-3idy: Crystal structure of HIV-gp120 core in complex with CD4-binding s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3idy
TitleCrystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C2221
Components
  • Fab b13 heavy chain
  • Fab b13 light chain
  • HIV-1 HxBc2 gp120 core
KeywordsIMMUNE SYSTEM / HIV-1 / antibody / gp120 / b13 / Envelope glycan protein / CD4-binding site / AIDS / Apoptosis / Cell membrane / Cleavage on pair of basic residues / Disulfide bond / Envelope protein / Fusion protein / Host-virus interaction / Membrane / Transmembrane / Viral immunoevasion / Virion
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / 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 ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / 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 / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChen, L. / Kwon, Y.D. / Zhou, T. / Wu, X. / O'Dell, S. / Cavacini, L. / Hessell, A.J. / Pancera, M. / Tang, M. / Xu, L. ...Chen, L. / Kwon, Y.D. / Zhou, T. / Wu, X. / O'Dell, S. / Cavacini, L. / Hessell, A.J. / Pancera, M. / Tang, M. / Xu, L. / Yang, Z.Y. / Zhang, M.Y. / Arthos, J. / Burton, D.R. / Dimitrov, D.S. / Nabel, G.J. / Posner, M. / Sodroski, J. / Wyatt, R. / Mascola, J.R. / Kwong, P.D.
CitationJournal: Science / Year: 2009
Title: Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120.
Authors: Chen, L. / Do Kwon, Y. / Zhou, T. / Wu, X. / O'Dell, S. / Cavacini, L. / Hessell, A.J. / Pancera, M. / Tang, M. / Xu, L. / Yang, Z.Y. / Zhang, M.Y. / Arthos, J. / Burton, D.R. / Dimitrov, D. ...Authors: Chen, L. / Do Kwon, Y. / Zhou, T. / Wu, X. / O'Dell, S. / Cavacini, L. / Hessell, A.J. / Pancera, M. / Tang, M. / Xu, L. / Yang, Z.Y. / Zhang, M.Y. / Arthos, J. / Burton, D.R. / Dimitrov, D.S. / Nabel, G.J. / Posner, M.R. / Sodroski, J. / Wyatt, R. / Mascola, J.R. / Kwong, P.D.
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 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 / 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 / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: HIV-1 HxBc2 gp120 core
H: Fab b13 heavy chain
L: Fab b13 light chain
A: HIV-1 HxBc2 gp120 core
B: Fab b13 heavy chain
C: Fab b13 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,44435
Polymers167,1546
Non-polymers6,29029
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.168, 204.316, 216.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain G and (resseq 83:119 or resseq 205:299 or resseq...
211chain A and (resseq 83:119 or resseq 205:299 or resseq...
112chain H and (resseq 1:101 or resid 110:231 ) and (not element H)
212chain B and (resseq 1:101 or resid 110:231 ) and (not element H)
113chain L and (resseq 1:29 or resseq 31:212 ) and (not element H)
213chain C and (resseq 1:29 or resseq 31:212 ) and (not element H)

NCS ensembles :
ID
1
2
3
DetailsThe biological assembly is an Antigen-Antibody complex that contains chain G in complex with chain H and L or chain A in complex with chain B and C.

-
Components

-
Antibody , 2 types, 4 molecules HBLC

#2: Antibody Fab b13 heavy chain


Mass: 24810.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1(-) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody Fab b13 light chain


Mass: 23639.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1(-) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 30 molecules GA

#1: Protein HIV-1 HxBc2 gp120 core


Mass: 35126.867 Da / Num. of mol.: 2
Mutation: M95W, T257S, S375W, A443M, W96C, V275C, I109C, Q428C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: HXBc2 / Gene: env / Plasmid: pcDNA3.1(-) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P04578*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.: 28
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

-
Non-polymers , 2 types, 153 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8 % PEG 8000, 6.5 % Isopropanol, 200 mM Ammonium sulfate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
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: Oct 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 35856 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Redundancy: 5.2 % / Rsym value: 0.099 / Net I/σ(I): 21.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.45 / % possible all: 34

-
Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IDX

3idx


Resolution: 3.2→43.204 Å / SU ML: -0 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 1778 5.03 %random
Rwork0.1955 ---
obs0.1977 35358 47.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 97.972 Å2 / ksol: 0.287 e/Å3
Refinement stepCycle: LAST / Resolution: 3.2→43.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11489 0 397 152 12038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412184
X-RAY DIFFRACTIONf_angle_d0.79616518
X-RAY DIFFRACTIONf_dihedral_angle_d15.9114424
X-RAY DIFFRACTIONf_chiral_restr0.0511895
X-RAY DIFFRACTIONf_plane_restr0.0042084
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11G2166X-RAY DIFFRACTIONPOSITIONAL
12A2166X-RAY DIFFRACTIONPOSITIONAL0.021
21H1662X-RAY DIFFRACTIONPOSITIONAL
22B1662X-RAY DIFFRACTIONPOSITIONAL0.013
31L1630X-RAY DIFFRACTIONPOSITIONAL
32C1630X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.28660.3897590.28561249X-RAY DIFFRACTION23
3.2866-3.38330.304920.27261815X-RAY DIFFRACTION33
3.3833-3.49240.2931240.24652233X-RAY DIFFRACTION41
3.4924-3.61720.28121350.2252565X-RAY DIFFRACTION47
3.6172-3.76190.27491390.20852732X-RAY DIFFRACTION50
3.7619-3.9330.22641550.19262822X-RAY DIFFRACTION51
3.933-4.14020.2131580.17192795X-RAY DIFFRACTION52
4.1402-4.39940.18141340.16272886X-RAY DIFFRACTION52
4.3994-4.73870.20541530.14682841X-RAY DIFFRACTION52
4.7387-5.21480.20661530.14492875X-RAY DIFFRACTION52
5.2148-5.96780.23261530.16332873X-RAY DIFFRACTION53
5.9678-7.51230.24981450.20382931X-RAY DIFFRACTION53
7.5123-43.20830.23311780.21932963X-RAY DIFFRACTION54
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.96920.1442-0.2274-0.7162-0.29812.9942-0.17950.2881-0.3859-0.0066-0.14390.00430.08730.2210.26810.91860.08630.24811.02940.07941.074675.689849.579121.014
22.11880.8261-0.42741.9199-1.16881.0316-0.0926-0.0682-0.10290.177-0.1099-0.2282-0.07540.51270.22180.8725-0.02130.081.41980.11950.886
34.63111.42920.24555.50352.27170.8216-0.3960.0431-0.2159-0.56920.7279-0.1566-0.14730.4277-0.22840.9543-0.317-0.02320.7283-0.04730.4347
42.71622.4790.17821.8682.92484.760.59930.1321-0.65741.3308-0.239-0.54451.8477-0.4149-0.18261.8282-0.1033-0.00451.3569-0.24161.4177
52.31411.5251-2.57785.29941.94584.3450.09620.3851-0.0223-0.42280.25310.142-0.7959-0.1132-0.27660.967-0.21570.10861.0669-0.13260.7036
61.9310.84620.77541.32860.6493-3.9443-0.06230.2560.2478-1.08960.2814-0.131-0.769-0.2872-0.21632.0558-0.290.35141.5749-0.13410.7969
70.88750.1012-0.02350.3665-1.0583.8151-0.3364-0.3920.099-0.11140.16370.02590.1371-0.46980.17631.07270.08410.00081.256-0.05990.9867
80.7947-0.84110.57462.82521.15331.5285-0.286-0.2104-0.23920.0753-0.00330.3591-0.2524-0.43920.22190.93650.2025-0.02931.3387-0.17441.0494
92.9075-1.07181.42080.75710.0332.2011-0.3186-0.1229-0.74420.59720.1670.0954-0.1569-0.27830.07161.8430.3301-0.49880.9466-0.08141.0413
100.82410.397-0.51493.5896-1.05442.68020.5247-0.19810.65831.8826-0.07871.15060.09780.1868-0.36592.14420.0020.17091.62670.17511.8958
112.2962-1.98010.05354.6677-0.07671.6794-0.2097-0.255-0.10941.14160.2448-0.03180.18250.2369-0.06751.73240.3382-0.22591.278-0.01131.057
122.7367-0.8147-1.8466-0.0148-2.3787-6.09720.5421-0.31150.17452.0983-0.0712-0.1622-1.68360.3284-0.28733.7005-0.11580.23621.71780.05630.8842
Refinement TLS groupSelection details: chain C and resid 110:214

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more