[English] 日本語
Yorodumi
- PDB-2n55: Structure of constitutively monomeric CXCL12 in complex with the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n55
TitleStructure of constitutively monomeric CXCL12 in complex with the CXCR4 N-terminus
Components
  • C-X-C chemokine receptor type 4
  • Stromal cell-derived factor 1
KeywordsCYTOKINE/Signaling Protein / CXL12 / CXCR4 / chemokine / GPCR / SDF1 / CYTOKINE-Signaling Protein complex
Function / homology
Function and homology information


C-X-C motif chemokine 12 receptor activity / regulation of viral process / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of vascular wound healing / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus ...C-X-C motif chemokine 12 receptor activity / regulation of viral process / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of vascular wound healing / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus / telencephalon cell migration / regulation of actin polymerization or depolymerization / C-X-C chemokine receptor activity / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / myosin light chain binding / myelin maintenance / positive regulation of vasculature development / regulation of programmed cell death / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / C-C chemokine receptor activity / endothelial tube morphogenesis / positive regulation of dopamine secretion / endothelial cell differentiation / C-C chemokine binding / Signaling by ROBO receptors / positive regulation of chemotaxis / regulation of chemotaxis / cellular response to organonitrogen compound / Formation of definitive endoderm / induction of positive chemotaxis / integrin activation / positive regulation of dendrite extension / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / anchoring junction / chemokine-mediated signaling pathway / blood circulation / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / positive regulation of calcium ion import / epithelial cell development / cellular response to cytokine stimulus / cell leading edge / detection of temperature stimulus involved in sensory perception of pain / small molecule binding / regulation of calcium ion transport / positive regulation of cell adhesion / positive regulation of T cell migration / Binding and entry of HIV virion / animal organ regeneration / Nuclear signaling by ERBB4 / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / regulation of cell adhesion / cardiac muscle contraction / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / neurogenesis / cell chemotaxis / adult locomotory behavior / response to activity / ubiquitin binding / G protein-coupled receptor activity / axon guidance / calcium-mediated signaling / brain development / neuron migration / response to virus / growth factor activity / defense response / intracellular calcium ion homeostasis / response to peptide hormone / chemotaxis / cellular response to xenobiotic stimulus / late endosome / integrin binding / virus receptor activity / actin binding / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cytoplasmic vesicle / collagen-containing extracellular matrix / Estrogen-dependent gene expression / lysosome / response to hypoxia / early endosome / cell adhesion / positive regulation of cell migration / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane
Similarity search - Function
CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / Stromal cell-derived factor 1 / CXC Chemokine domain / Chemokine receptor family / 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 ...CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / Stromal cell-derived factor 1 / CXC Chemokine domain / Chemokine receptor family / 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
Stromal cell-derived factor 1 / C-X-C chemokine receptor type 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model1
AuthorsZiarek, J.J. / Peterson, F.C. / Volkman, B.F.
CitationJournal: Sci Signal / Year: 2017
Title: Structural basis for chemokine recognition by a G protein-coupled receptor and implications for receptor activation.
Authors: Ziarek, J.J. / Kleist, A.B. / London, N. / Raveh, B. / Montpas, N. / Bonneterre, J. / St-Onge, G. / DiCosmo-Ponticello, C.J. / Koplinski, C.A. / Roy, I. / Stephens, B. / Thelen, S. / ...Authors: Ziarek, J.J. / Kleist, A.B. / London, N. / Raveh, B. / Montpas, N. / Bonneterre, J. / St-Onge, G. / DiCosmo-Ponticello, C.J. / Koplinski, C.A. / Roy, I. / Stephens, B. / Thelen, S. / Veldkamp, C.T. / Coffman, F.D. / Cohen, M.C. / Dwinell, M.B. / Thelen, M. / Peterson, F.C. / Heveker, N. / Volkman, B.F.
History
DepositionJul 7, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 1.3May 3, 2017Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Stromal cell-derived factor 1
B: C-X-C chemokine receptor type 4


Theoretical massNumber of molelcules
Total (without water)12,6652
Polymers12,6652
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3281.2 Å2
ΔGint-10.4 kcal/mol
Surface area7408.4 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Stromal cell-derived factor 1 / / SDF-1 / hSDF-1 / C-X-C motif chemokine 12 / Intercrine reduced in hepatomas / IRH / hIRH / Pre-B ...SDF-1 / hSDF-1 / C-X-C motif chemokine 12 / Intercrine reduced in hepatomas / IRH / hIRH / Pre-B cell growth-stimulating factor / PBSF / SDF-1-beta(3-72) / SDF-1-alpha(3-67)


Mass: 8146.680 Da / Num. of mol.: 1 / Mutation: L76C, I79C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P48061
#2: Protein/peptide C-X-C chemokine receptor type 4 / CXC-R4 / CXCR-4 / FB22 / Fusin / HM89 / LCR1 / Leukocyte-derived seven transmembrane domain ...CXC-R4 / CXCR-4 / FB22 / Fusin / HM89 / LCR1 / Leukocyte-derived seven transmembrane domain receptor / LESTR / Lipopolysaccharide-associated protein 3 / LAP-3 / LPS-associated protein 3 / NPYRL / Stromal cell-derived factor 1 receptor / SDF-1 receptor


Mass: 4518.772 Da / Num. of mol.: 1 / Mutation: C28A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCR4 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P61073

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1423D 1H-15N NOESY
1523D 1H-13C NOESY aliphatic
1623D 1H-13C NOESY aromatic
1713D F1-13C filtered/F3-13C edited NOESY aliphatic
1823D F1-13C filtered/F3-13C edited NOESY aliphatic

-
Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-99% 13C; U-99% 15N] protein_1, 25 mM [U-2H] MES, 10 % [U-99% 2H] D2O, 0.02 % sodium azide, 2 mM protein_2, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] protein_2, 25 mM [U-2H] MES, 0.02 % sodium azide, 10 % [U-99% 2H] D2O, 2 mM protein_1, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity_1-1[U-99% 13C; U-99% 15N]1
25 mMMES-2[U-2H]1
10 %D2O-3[U-99% 2H]1
0.02 %sodium azide-41
2 mMentity_2-51
1 mMentity_2-6[U-99% 13C; U-99% 15N]2
25 mMMES-7[U-2H]2
0.02 %sodium azide-82
10 %D2O-9[U-99% 2H]2
2 mMentity_1-102
Sample conditionsIonic strength: 0.02 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
XEASYBartels et al.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
GARANTBartels, Guntert, Billeter and Wuthrichchemical shift assignment
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1533 / NOE intraresidue total count: 365 / NOE long range total count: 486 / NOE medium range total count: 241 / NOE sequential total count: 441 / Protein phi angle constraints total count: 57 / Protein psi angle constraints total count: 52
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

+
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