[English] 日本語
Yorodumi
- PDB-5uiw: Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uiw
TitleCrystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV entry inhibitor 5P7-CCL5
Components
  • C-C chemokine receptor type 5,Rubredoxin chimera
  • C-C motif chemokine 5
KeywordsSIGNALING PROTEIN / G-protein coupled receptor / Chemokine receptor / HIV entry inhibitor / HIV-1 R5 isolates co-receptor / receptor-ligand complex
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine (C-C motif) ligand 5 signaling pathway / activation of phospholipase D activity / chemokine receptor antagonist activity / chemokine (C-C motif) ligand 5 binding / : / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine (C-C motif) ligand 5 signaling pathway / activation of phospholipase D activity / chemokine receptor antagonist activity / chemokine (C-C motif) ligand 5 binding / : / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / alkane catabolic process / receptor signaling protein tyrosine kinase activator activity / chemokine receptor activity / CCR5 chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of receptor signaling pathway via STAT / positive regulation of homotypic cell-cell adhesion / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / signaling / neutrophil activation / positive regulation of G protein-coupled receptor signaling pathway / C-C chemokine receptor activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / C-C chemokine binding / eosinophil chemotaxis / cell surface receptor signaling pathway via STAT / positive regulation of calcium ion transport / response to cholesterol / positive regulation of monocyte chemotaxis / positive regulation of innate immune response / chemokine-mediated signaling pathway / chemokine activity / regulation of T cell activation / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / negative regulation of G protein-coupled receptor signaling pathway / leukocyte cell-cell adhesion / negative regulation of viral genome replication / phospholipase activator activity / positive regulation of smooth muscle cell migration / positive regulation of macrophage chemotaxis / chemoattractant activity / macrophage chemotaxis / exocytosis / monocyte chemotaxis / Interleukin-10 signaling / positive regulation of translational initiation / cellular response to interleukin-1 / cellular response to fibroblast growth factor stimulus / negative regulation by host of viral transcription / positive regulation of T cell migration / Binding and entry of HIV virion / positive regulation of phosphorylation / cellular defense response / positive regulation of viral genome replication / coreceptor activity / positive regulation of T cell proliferation / positive regulation of cell adhesion / regulation of insulin secretion / positive regulation of epithelial cell proliferation / epithelial cell proliferation / cell chemotaxis / positive regulation of smooth muscle cell proliferation / calcium-mediated signaling / response to virus / cellular response to type II interferon / cellular response to virus / intracellular calcium ion homeostasis / response to toxic substance / calcium ion transport / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / MAPK cascade / cellular response to tumor necrosis factor / cell-cell signaling / actin binding / virus receptor activity / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / G alpha (i) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / electron transfer activity / cell surface receptor signaling pathway / protein kinase activity / endosome / positive regulation of cell migration / immune response / G protein-coupled receptor signaling pathway / inflammatory response / iron ion binding / external side of plasma membrane / apoptotic process / cell surface / protein homodimerization activity / extracellular space
Similarity search - Function
CC chemokine receptor 5 / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine receptor family ...CC chemokine receptor 5 / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine receptor family / Rubredoxin-like domain / Rubredoxin-like domain profile. / : / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Rubredoxin / C-C motif chemokine 5 / C-C chemokine receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.204 Å
AuthorsZheng, Y. / Qin, L. / Han, G.W. / Gustavsson, M. / Kawamura, T. / Stevens, R.C. / Cherezov, V. / Kufareva, I. / Handel, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118985 United States
CitationJournal: Immunity / Year: 2017
Title: Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV.
Authors: Zheng, Y. / Han, G.W. / Abagyan, R. / Wu, B. / Stevens, R.C. / Cherezov, V. / Kufareva, I. / Handel, T.M.
History
DepositionJan 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Dec 11, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_target_identifier / _pdbx_audit_support.funding_organization
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-C chemokine receptor type 5,Rubredoxin chimera
B: C-C motif chemokine 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,59111
Polymers55,8212
Non-polymers2,7709
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-12 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.010, 52.640, 302.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein C-C chemokine receptor type 5,Rubredoxin chimera / CCR5 / CHEMR13 / HIV-1 fusion coreceptor / Rd / CCR5 / CHEMR13 / HIV-1 fusion coreceptor


Mass: 47158.828 Da / Num. of mol.: 1 / Mutation: C58Y, G163N, A233D, K303E
Source method: isolated from a genetically manipulated source
Details: Rubredoxin fusion sequence P00268; in between CCR5 residue 223 and 227 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEE
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: CCR5, CMKBR5 / Plasmid: pfastbac-1 / Cell line (production host): sf9 / Organ (production host): Ovary / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P51681, UniProt: P00268
#2: Protein C-C motif chemokine 5 / EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific ...EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific protein P228 / TCP228 / T-cell-specific protein RANTES


Mass: 8662.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence before CC motif "QGPPLMALQS" (where the first residue Q is PCA as glutamine is cyclized into pyroglutamic acid residue) is artificial to replace native sequence "SPYSSDTTP". As the ...Details: Sequence before CC motif "QGPPLMALQS" (where the first residue Q is PCA as glutamine is cyclized into pyroglutamic acid residue) is artificial to replace native sequence "SPYSSDTTP". As the register 0 for PCA, all the rest of residue numbers are consistent for chemokine residues.
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Plasmid: pfastbac-1 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13501

-
Non-polymers , 4 types, 53 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 295.5 K / Method: lipidic cubic phase / pH: 6.3
Details: 29% (v/v) PEG 400, 120 mM lithium citrate, 1.2% (w/v) 1,5-Diaminopentane dihydrochloride, 100 mM 2-(N-morpholino)ethanesulfonic acid

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2016 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.18→29.472 Å / Num. obs: 32803 / % possible obs: 99.2 % / Redundancy: 13.7 % / Biso Wilson estimate: 28.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.039 / Rrim(I) all: 0.151 / Net I/av σ(I): 9.4 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.18-2.257.42.2920.625750.6440.7992.43791.3
8.99-46.6711.60.05136.55790.9990.0160.05499.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.9refinement
Aimless0.1.29data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MBS

4mbs


Resolution: 2.204→29.472 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.72
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 1196 5.1 %Random selection
Rwork0.2158 ---
obs0.2176 23465 73.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.87 Å2 / Biso mean: 42.3057 Å2 / Biso min: 5.5 Å2
Refinement stepCycle: final / Resolution: 2.204→29.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 124 44 3437
Biso mean--59.43 33.79 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063491
X-RAY DIFFRACTIONf_angle_d0.9694722
X-RAY DIFFRACTIONf_chiral_restr0.035539
X-RAY DIFFRACTIONf_plane_restr0.005582
X-RAY DIFFRACTIONf_dihedral_angle_d15.1021218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2036-2.29180.329260.270732435010
2.2918-2.39610.3529650.26871165123035
2.3961-2.52230.27651080.2541772188054
2.5223-2.68030.29371270.25692315244271
2.6803-2.8870.30311330.24852945307887
2.887-3.17730.28381750.25213349352499
3.1773-3.63630.24871680.216433623530100
3.6363-4.57860.24731770.185934353612100
4.5786-29.47460.20222170.192936023819100
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)
11.8342-0.0167-1.23911.65471.91513.02540.07230.62940.3912-0.48360.0168-0.0362-0.5779-0.0707-0.24810.1809-0.04130.00450.57470.08140.1637-132.3783-94.8877611.2836
21.1851-0.1183-0.13591.08230.51611.5743-0.21340.01070.00440.33150.03730.07660.14710.004-0.08890.12910.04860.02670.286-0.04630.1217-133.5119-97.4485642.3796
30.92350.901-0.61382.6023-2.78133.2562-0.18270.2252-0.3645-1.1064-0.1435-0.43231.24920.14160.2980.9807-0.03080.13170.38490.09360.3185-140.0878-122.1137683.0264
42.15610.04540.24611.4603-0.53681.664-0.1376-0.1311-0.01790.42650.06290.24390.4221-0.32620.11960.2582-0.05120.11370.231-0.01480.1808-141.3603-104.9308644.9275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 0 through 67 )B0 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 223 )A16 - 223
3X-RAY DIFFRACTION3chain 'A' and (resid 1001 through 1054 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 227 through 316 )A227 - 316

+
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