[English] 日本語
Yorodumi
- PDB-2ra4: Crystal Structure of Human Monocyte Chemoattractant Protein 4 (MC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ra4
TitleCrystal Structure of Human Monocyte Chemoattractant Protein 4 (MCP-4/CCL13)
ComponentsSmall-inducible cytokine A13
KeywordsCYTOKINE / CCL13 / MCP-4 / CC chemokine family / chemotaxis / monocytes / Inflammatory response / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / chemokine activity / Chemokine receptors bind chemokines / cytoskeleton organization / intracellular calcium ion homeostasis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling ...CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / chemokine activity / Chemokine receptors bind chemokines / cytoskeleton organization / intracellular calcium ion homeostasis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / regulation of cell shape / G alpha (i) signalling events / killing of cells of another organism / positive regulation of cell migration / inflammatory response / signaling receptor binding / signal transduction / extracellular space / extracellular region
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / 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
trifluoroacetic acid / C-C motif chemokine 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLubkowski, J. / Barinka, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of human monocyte chemoattractant protein 4 (MCP-4/CCL13).
Authors: Barinka, C. / Prahl, A. / Lubkowski, J.
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small-inducible cytokine A13
B: Small-inducible cytokine A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1859
Polymers17,4952
Non-polymers6907
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
MethodPISA
2
A: Small-inducible cytokine A13
B: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
B: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
B: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
B: Small-inducible cytokine A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,74136
Polymers69,9798
Non-polymers2,76228
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area26260 Å2
MethodPISA
3
A: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
hetero molecules

A: Small-inducible cytokine A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,14216
Polymers34,9904
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area7040 Å2
MethodPISA
4
B: Small-inducible cytokine A13
hetero molecules

B: Small-inducible cytokine A13
hetero molecules

B: Small-inducible cytokine A13
hetero molecules

B: Small-inducible cytokine A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,59820
Polymers34,9904
Non-polymers1,60916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.673, 74.673, 51.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11B-78-

SO4

21B-78-

SO4

-
Components

#1: Protein Small-inducible cytokine A13 / CCL13 / Monocyte chemotactic protein 4 / MCP-4 / Monocyte chemoattractant protein 4 / CK-beta-10 / NCC-1


Mass: 8747.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL13, MCP4, NCC1, SCYA13 / Plasmid: pET-11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)trxB / References: UniProt: Q99616
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, 2 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 15683 / Num. obs: 15683 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 26.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1dok

1dok


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.106 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21581 783 5 %RANDOM
Rwork0.17974 ---
obs0.18155 14898 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.722 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 37 72 1147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221153
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9861555
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.3822.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93815239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.215158
X-RAY DIFFRACTIONr_chiral_restr0.1490.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02782
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2483
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2760
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4941.5689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.19821100
X-RAY DIFFRACTIONr_scbond_it3.3833522
X-RAY DIFFRACTIONr_scangle_it4.6874.5455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 54 -
Rwork0.233 1073 -
obs--99.38 %
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)
12.49831.05911.29862.01820.92333.1448-0.03710.01180.01310.17790.0244-0.00230.0480.0740.0127-0.06660.0252-0.0065-0.08180.0068-0.067150.602528.144325.3157
24.89070.04642.14360.8923-0.03863.49430.08570.3958-0.1217-0.14-0.10410.17750.13850.00740.0184-0.04790.0214-0.0053-0.0339-0.0398-0.039739.930121.29124.9028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 674 - 68
2X-RAY DIFFRACTION2BB3 - 674 - 68

+
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