[English] 日本語
Yorodumi
- PDB-2k01: Structure of a locked SDF1 dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k01
TitleStructure of a locked SDF1 dimer
ComponentsStromal cell-derived factor 1
KeywordsCYTOKINE / stromal cell derived factor-1 / SDF1-alpha / CXCL12 / chemokine / sulfotyrosine / locked dimer / Alternative splicing / Chemotaxis / Growth factor / Secreted
Function / homology
Function and homology information


telencephalon cell migration / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / regulation of actin polymerization or depolymerization / chemokine receptor binding / CXCL12-activated CXCR4 signaling pathway / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of vasculature development ...telencephalon cell migration / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / regulation of actin polymerization or depolymerization / chemokine receptor binding / CXCL12-activated CXCR4 signaling pathway / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of vasculature development / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / integrin activation / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to chemokine / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / chemokine activity / blood circulation / Chemokine receptors bind chemokines / positive regulation of calcium ion import / detection of temperature stimulus involved in sensory perception of pain / animal organ regeneration / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of T cell migration / Nuclear signaling by ERBB4 / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / positive regulation of cell adhesion / axon guidance / adult locomotory behavior / cell chemotaxis / growth factor activity / defense response / response to peptide hormone / response to virus / integrin binding / neuron migration / intracellular calcium ion homeostasis / chemotaxis / : / G alpha (i) signalling events / Estrogen-dependent gene expression / response to hypoxia / cell adhesion / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / signaling receptor binding / external side of plasma membrane / signal transduction / extracellular exosome / extracellular region
Similarity search - Function
CXC Chemokine domain / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Stromal cell-derived factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
AuthorsVolkman, B.F. / Veldkamp, C.T. / Peterson, F.C.
CitationJournal: Sci.Signal. / Year: 2008
Title: Structural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12
Authors: Veldkamp, C.T. / Seibert, C. / Peterson, F.C. / De la Cruz, N.B. / Haugner, J.C. / Basnet, H. / Sakmar, T.P. / Volkman, B.F.
History
DepositionJan 23, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Stromal cell-derived factor 1
C: Stromal cell-derived factor 1


Theoretical massNumber of molelcules
Total (without water)16,3782
Polymers16,3782
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Stromal cell-derived factor 1 / SDF-1 / C-X-C motif chemokine 12 / Pre-B cell growth-stimulating factor / PBSF / hIRH


Mass: 8188.760 Da / Num. of mol.: 2 / Fragment: SDF-1-alpha(3-67) domain / Mutation: L36C,A65C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Production host: Escherichia coli (E. coli) / Strain (production host): SG130099[pREP4] / References: UniProt: P48061
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)

-
Sample preparation

DetailsContents: 0.620 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.620 mM / Component: CXCL12/SDF1-alpha / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 21 / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
XwinNMR3.5Brukercollection
NMRPipe2004Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
SPSCAN1.1.0R.W. Glaserdata analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, AUTOMATED METHODS WERE ...Method: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: CXCL12 DIMER STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND ...Details: CXCL12 DIMER STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 138 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED IN ONE CXCL12/CXCR4 COMPLEX AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND COMPLEX. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS., CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 138 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED IN ONE CXCL12/CXCR4 COMPLEX AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND COMPLEX. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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