[English] 日本語
Yorodumi
- PDB-4oij: X-ray crystal structure of racemic non-glycosylated chemokine Ser-CCL1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oij
TitleX-ray crystal structure of racemic non-glycosylated chemokine Ser-CCL1
Components
  • C-C motif chemokine 1Chemokine
  • D-Ser-CCL1
KeywordsSIGNALING PROTEIN / Chemical protein synthesis / racemic protein crystallography / Glycoprotein / Chemokine
Function / homology
Function and homology information


CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of interleukin-17 production / monocyte chemotaxis / cellular response to interleukin-1 ...CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of interleukin-17 production / monocyte chemotaxis / cellular response to interleukin-1 / viral process / neutrophil chemotaxis / cellular response to type II interferon / positive regulation of inflammatory response / intracellular calcium ion homeostasis / chemotaxis / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / positive regulation of ERK1 and ERK2 cascade / inflammatory response / G protein-coupled receptor signaling pathway / 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
polypeptide(D) / polypeptide(D) (> 10) / C-C motif chemokine 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOkamoto, R. / Mandal, K. / Sawaya, M.R. / Kajihara, Y. / Yeates, T.O. / Kent, S.B.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: (Quasi-)Racemic X-ray Structures of Glycosylated and Non-Glycosylated Forms of the Chemokine Ser-CCL1 Prepared by Total Chemical Synthesis.
Authors: Okamoto, R. / Mandal, K. / Sawaya, M.R. / Kajihara, Y. / Yeates, T.O. / Kent, S.B.
History
DepositionJan 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-C motif chemokine 1
B: C-C motif chemokine 1
C: D-Ser-CCL1
D: D-Ser-CCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,34135
Polymers34,3634
Non-polymers2,97831
Water2,162120
1
A: C-C motif chemokine 1
B: C-C motif chemokine 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,82119
Polymers17,1882
Non-polymers1,63317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-23 kcal/mol
Surface area9190 Å2
MethodPISA
2
C: D-Ser-CCL1
D: D-Ser-CCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,51916
Polymers17,1742
Non-polymers1,34514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-14 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.480, 48.860, 51.050
Angle α, β, γ (deg.)109.46, 106.84, 109.00
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein C-C motif chemokine 1 / Chemokine / Small-inducible cytokine A1 / T lymphocyte-secreted protein I-309


Mass: 8594.190 Da / Num. of mol.: 2 / Fragment: UNP residues 23-96 / Source method: obtained synthetically / Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P22362
#2: Protein D-Ser-CCL1


Mass: 8587.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical Synthesis / Source: (synth.) synthetic construct (others)
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 2 M Ammonium Sulfate, 0.1 M citric acid, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16601 / % possible obs: 75.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 22.13 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.4
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 0.3 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.2 / Num. unique all: 121 / % possible all: 8.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→18.86 Å / Cor.coef. Fo:Fc: 0.9172 / Cor.coef. Fo:Fc free: 0.8861 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 837 5.04 %RANDOM
Rwork0.2338 ---
obs0.2363 16601 --
Displacement parametersBiso mean: 49.51 Å2
Baniso -1Baniso -2Baniso -3
1--5.1559 Å21.5458 Å2-0.2927 Å2
2--9.3067 Å2-0.9955 Å2
3----4.1507 Å2
Refine analyzeLuzzati coordinate error obs: 0.438 Å
Refinement stepCycle: LAST / Resolution: 2→18.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 155 120 2517
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012514HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.153402HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d612SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes364HARMONIC5
X-RAY DIFFRACTIONt_it2514HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion22.01
X-RAY DIFFRACTIONt_chiral_improper_torsion295SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2332SEMIHARMONIC4
LS refinement shellResolution: 2→2.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.215 31 6.11 %
Rwork0.1951 476 -
all0.1964 507 -
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)
117.4988-2.65370.93643.2617-2.67275.3963-0.2011-1.0757-1.36080.204-0.11040.12120.45840.45130.3115-0.22710.01550.03680.08320.1455-0.22314.06814.064232.4486
219.4619-2.7061-0.93143.56992.82195.2095-0.2439-1.16041.34990.17660.0121-0.121-0.392-0.36650.2318-0.21410.0282-0.0470.0722-0.1639-0.2286-11.947119.036932.442
316.1645-3.7419-1.96423.7512-0.96014.95440.40641.20781.2519-0.2060.0067-0.3043-0.3974-0.7385-0.4131-0.22520.05010.05780.16720.1876-0.19629.756419.406211.0235
415.8541-4.24650.73063.93450.78094.76870.41591.2461-1.1573-0.2526-0.02450.32440.35890.6873-0.3914-0.2460.0372-0.07850.1847-0.2157-0.199527.6093.732210.7926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|4 - A|74 }A4 - 74
2X-RAY DIFFRACTION2{ B|4 - B|74 }B4 - 74
3X-RAY DIFFRACTION3{ C|6 - C|57 C|58 - C|73 }C6 - 57
4X-RAY DIFFRACTION3{ C|6 - C|57 C|58 - C|73 }C58 - 73
5X-RAY DIFFRACTION4{ D|6 - D|57 D|58 - D|73 }D6 - 57
6X-RAY DIFFRACTION4{ D|6 - D|57 D|58 - D|73 }D58 - 73

+
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