[English] 日本語
Yorodumi
- PDB-4mbs: Crystal Structure of the CCR5 Chemokine Receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mbs
TitleCrystal Structure of the CCR5 Chemokine Receptor
ComponentsChimera protein of C-C chemokine receptor type 5 and Rubredoxin
KeywordsSIGNALING PROTEIN / Human CCR5 Chemokine Receptor / anti-HIV agent / novel protein engineering / GPCR network / membrane protein / PSI-Biology / Structural Genomics / Seven transmembrane helices / G protein-coupled receptor / membrane
Function / homology
Function and homology information


chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum ...chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / Interleukin-10 signaling / Binding and entry of HIV virion / cellular defense response / coreceptor activity / cell chemotaxis / calcium-mediated signaling / calcium ion transport / chemotaxis / MAPK cascade / virus receptor activity / cell-cell signaling / actin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cellular response to lipopolysaccharide / electron transfer activity / cell surface receptor signaling pathway / endosome / immune response / inflammatory response / iron ion binding / G protein-coupled receptor signaling pathway / external side of plasma membrane / cell surface / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
CC chemokine receptor 5 / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Chemokine receptor family / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rhopdopsin 7-helix transmembrane proteins ...CC chemokine receptor 5 / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Chemokine receptor family / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MRV / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Rubredoxin / C-C chemokine receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsTan, Q. / Zhu, Y. / Han, G.W. / Li, J. / Fenalti, G. / Liu, H. / Cherezov, V. / Stevens, R.C. / GPCR Network (GPCR) / Zhao, Q. / Wu, B.
CitationJournal: Science / Year: 2013
Title: Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex.
Authors: Tan, Q. / Zhu, Y. / Li, J. / Chen, Z. / Han, G.W. / Kufareva, I. / Li, T. / Ma, L. / Fenalti, G. / Li, J. / Zhang, W. / Xie, X. / Yang, H. / Jiang, H. / Cherezov, V. / Liu, H. / Stevens, R.C. / Zhao, Q. / Wu, B.
History
DepositionAug 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chimera protein of C-C chemokine receptor type 5 and Rubredoxin
B: Chimera protein of C-C chemokine receptor type 5 and Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,75616
Polymers95,0332
Non-polymers4,72414
Water86548
1
A: Chimera protein of C-C chemokine receptor type 5 and Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2359
Polymers47,5161
Non-polymers2,7188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chimera protein of C-C chemokine receptor type 5 and Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5227
Polymers47,5161
Non-polymers2,0056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.920, 103.520, 137.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

-
Components

#1: Protein Chimera protein of C-C chemokine receptor type 5 and Rubredoxin / / C-C CKR-5 / CC-CKR-5 / CCR-5 / CCR5 / CHEMR13 / HIV-1 fusion coreceptor


Mass: 47516.281 Da / Num. of mol.: 2
Fragment: Rubredoxin inserted into CCR5 between residue 223 and 227
Mutation: C58Y, G163N, A233D, K303E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: CCR5, CCR5_HUMAN, CMKBR5, Rd / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P51681, UniProt: P00268
#2: Chemical ChemComp-MRV / 4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]oct-8-yl}-1-phenylpropyl]cyclohexanecarboxamide / Maraviroc


Mass: 513.666 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H41F2N5O / Comment: medication, antiretroviral*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 32% PEG 400, 0.1M HEPES, 0.1M sodium chloride, pH 7.0, Lipidic cubic phase, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2013 / Details: 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: 2.7→50 Å / Num. all: 28947 / Num. obs: 27674 / % possible obs: 95.6 % / Redundancy: 6 % / Biso Wilson estimate: 67.63 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 14.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ODU

3odu


Resolution: 2.71→36.33 Å / Cor.coef. Fo:Fc: 0.9383 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.664 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1416 5.12 %RANDOM
Rwork0.2156 ---
obs0.2181 27630 95.47 %-
all-28941 --
Displacement parametersBiso mean: 72.95 Å2
Baniso -1Baniso -2Baniso -3
1-5.7134 Å20 Å20 Å2
2---3.7025 Å20 Å2
3----2.0109 Å2
Refine analyzeLuzzati coordinate error obs: 0.417 Å
Refinement stepCycle: LAST / Resolution: 2.71→36.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 0 230 48 5764
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015871HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.997980HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2586SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes845HARMONIC5
X-RAY DIFFRACTIONt_it5871HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion3.24
X-RAY DIFFRACTIONt_chiral_improper_torsion758SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6545SEMIHARMONIC4
LS refinement shellResolution: 2.71→2.81 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2411 145 5.36 %
Rwork0.2191 2561 -
all0.2203 2706 -
obs--95.47 %
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)
11.7832-0.08970.18851.57331.30453.1921-0.07290.1339-0.1459-0.01370.00640.0202-0.0063-0.00320.0665-0.2472-0.0412-0.01980.0671-0.0554-0.262147.597107.79833.5432
27.74360.32541.19475.45590.5886.8399-0.09030.14690.2164-0.0811-0.0964-0.0847-0.01470.03450.1867-0.048-0.0226-0.02530.04690.0346-0.3032152.514140.22866.1547
31.71310.47730.79251.0260.71184.7541-0.06110.26320.06160.03450.0885-0.095-0.17950.0955-0.0274-0.1915-0.0636-0.02380.1028-0.0128-0.2434155.465116.42336.0787
41.6630.38010.52161.83571.40663.6221-0.0950.1137-0.0904-0.04980.04140.0302-0.0932-0.06270.0536-0.2691-0.0432-0.02270.0635-0.036-0.2734183.232111.22233.9726
56.5090.44080.91188.3076-2.1646.1615-0.02520.15890.20730.2778-0.2121-0.3643-0.0418-0.04180.2373-0.0785-0.016-0.04580.04610.0411-0.304189.455143.73666.0225
61.58740.3267-0.251.72880.80222.7532-0.16250.27380.1139-0.10670.2318-0.0961-0.30250.1312-0.0693-0.178-0.12170.00750.1782-0.0474-0.304191.37119.44736.1572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 22319 - 223
2X-RAY DIFFRACTION2AA1001 - 10541001 - 1054
3X-RAY DIFFRACTION3AA227 - 313227 - 313
4X-RAY DIFFRACTION4BB19 - 22319 - 223
5X-RAY DIFFRACTION5BB1001 - 10541001 - 1054
6X-RAY DIFFRACTION6BB227 - 313227 - 313

+
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