[English] 日本語
Yorodumi
- PDB-2qad: Structure of tyrosine-sulfated 412d antibody complexed with HIV-1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qad
TitleStructure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4
Components
  • (anti-HIV-1 antibody 412d ...) x 2
  • Envelope glycoprotein gp160
  • T-cell surface glycoprotein CD4
Keywordsviral protein/immune system / viral protein-immune system complex
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 / Dectin-2 family / immunoglobulin complex / 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 / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / protein tyrosine kinase binding / positive regulation of establishment of T cell polarity / positive regulation of interleukin-2 production / virus-mediated perturbation of host defense response / T cell activation / host cell endosome membrane / 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 / clathrin-dependent endocytosis of virus by host cell / 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 / viral protein processing / early endosome / cell adhesion / immune response / positive regulation of protein phosphorylation / membrane raft / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / structural molecule activity / virion attachment to host cell / endoplasmic reticulum membrane / protein kinase binding / host cell plasma membrane / virion membrane / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / extracellular region / membrane / 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 / 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 subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
MALONIC ACID / Immunoblobulin G1 Fab heavy chain variable region / T-cell surface glycoprotein CD4 / Envelope glycoprotein gp160 / :
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHuang, C.-C. / Tang, M. / Robinson, J. / Wyatt, R. / Kwong, P.D.
CitationJournal: Science / Year: 2007
Title: Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4
Authors: Huang, C.-C. / Lam, S.N. / Acharya, P. / Tang, M. / Xiang, S.-H. / Hussan, S.S. / Stanfield, R.L. / Robinson, J. / Sodroski, J. / Wilson, I.A. / Wyatt, R. / Bewley, C.A. / Kwong, P.D.
History
DepositionJun 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / 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_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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Aug 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
Revision 1.8Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein gp160
B: T-cell surface glycoprotein CD4
C: anti-HIV-1 antibody 412d light chain
D: anti-HIV-1 antibody 412d heavy chain
E: Envelope glycoprotein gp160
F: T-cell surface glycoprotein CD4
G: anti-HIV-1 antibody 412d light chain
H: anti-HIV-1 antibody 412d heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,73850
Polymers209,0298
Non-polymers7,70842
Water0
1
A: Envelope glycoprotein gp160
B: T-cell surface glycoprotein CD4
C: anti-HIV-1 antibody 412d light chain
D: anti-HIV-1 antibody 412d heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,51026
Polymers104,5154
Non-polymers3,99622
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Envelope glycoprotein gp160
F: T-cell surface glycoprotein CD4
G: anti-HIV-1 antibody 412d light chain
H: anti-HIV-1 antibody 412d heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,22724
Polymers104,5154
Non-polymers3,71220
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.600, 53.021, 225.326
Angle α, β, γ (deg.)90.00, 104.64, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthis entry contains the crystallographic asymmetric unit which consists of two gp120/cd4/412d complexes. chain A, B, C, and D form one complex, and chain E, F, G, and H form the other.

-
Components

-
Protein , 2 types, 4 molecules AEBF

#1: Protein Envelope glycoprotein gp160 / Env polyprotein


Mass: 36062.059 Da / Num. of mol.: 2 / Fragment: CORE WITH V3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: YU2 / Gene: env / Plasmid: CMVR / Cell line (production host): EMBRYONIC CELL LINE 293 / Production host: Homo sapiens (human) / References: UniProt: P35961
#2: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 20129.896 Da / Num. of mol.: 2
Fragment: D1D2, IG-LIKE V-TYPE AND IG-LIKE C2-TYPE 1 DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: Escherichia coli (E. coli) / References: UniProt: P01730

-
Antibody , 2 types, 4 molecules CGDH

#3: Antibody anti-HIV-1 antibody 412d light chain


Mass: 23483.066 Da / Num. of mol.: 2 / Fragment: FAB, ANTIGEN-BINDING FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus / Production host: Human herpesvirus 4 (Epstein-Barr virus) / Strain (production host): Epstein-barr virus / References: UniProt: Q6GMX8
#4: Antibody anti-HIV-1 antibody 412d heavy chain


Mass: 24839.684 Da / Num. of mol.: 2 / Fragment: FAB, ANTIGEN-BINDING FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus / Production host: Human herpesvirus 4 (Epstein-Barr virus) / Strain (production host): Epstein-barr virus / References: UniProt: A4F255

-
Sugars , 1 types, 31 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.: 31
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, 11 molecules

#6: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17-19% polyethylene glycol (PEG) 1500, 0.1 M Na cacodylate pH 6.5, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2004
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 25816 / % possible obs: 67.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 9.1
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.3 / Num. unique all: 595 / % possible all: 16.2

-
Processing

Software
NameClassification
PHENIXrefinement
AMoREphasing
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG

1rzk

412d

1rzg


Resolution: 3.3→20 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: TLS refinement was performed with PHENIX. 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 ...Details: TLS refinement was performed with PHENIX. 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% reflectionSelection details
Rfree0.269 1329 5 %random
Rwork0.202 ---
all-38401 --
obs-25600 66.7 %-
Displacement parametersBiso mean: 156 Å2
Baniso -1Baniso -2Baniso -3
1--46.386 Å20 Å2-20.021 Å2
2--16.91 Å20 Å2
3---29.475 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.53 Å
Luzzati d res low-20 Å
Luzzati sigma a0.84 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14497 0 490 0 14987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.0054
X-RAY DIFFRACTIONf_angle_deg1.092

+
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