[English] 日本語
Yorodumi
- PDB-1fbm: ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN IN COMPLEX... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fbm
TitleASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN IN COMPLEX WITH ALL-TRANS RETINOL
ComponentsPROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
KeywordsCELL ADHESION / EXTRACELLULAR MATRIX PROTEIN / ASSEMBLY DOMAIN / CARTILAGE / OLIGOMERIC MATRIX PROTEIN / GLYCOPROTEIN / RETINOL-COMPLEX
Function / homology
Function and homology information


tendon development / negative regulation of hemostasis / cartilage homeostasis / Integrin cell surface interactions / ECM proteoglycans / vascular associated smooth muscle contraction / chondrocyte development / bone growth / vascular associated smooth muscle cell development / musculoskeletal movement ...tendon development / negative regulation of hemostasis / cartilage homeostasis / Integrin cell surface interactions / ECM proteoglycans / vascular associated smooth muscle contraction / chondrocyte development / bone growth / vascular associated smooth muscle cell development / musculoskeletal movement / BMP binding / chondrocyte proliferation / growth plate cartilage development / endochondral bone growth / positive regulation of chondrocyte proliferation / vitamin D binding / regulation of bone mineralization / muscle cell development / heparan sulfate proteoglycan binding / bone morphogenesis / cartilage development / collagen fibril organization / proteoglycan binding / limb development / artery morphogenesis / extracellular matrix structural constituent / neuromuscular process / skin development / bone mineralization / fibronectin binding / protein secretion / response to unfolded protein / BMP signaling pathway / collagen binding / extracellular matrix / ossification / skeletal system development / protein homooligomerization / protein processing / platelet aggregation / multicellular organism growth / integrin binding / blood coagulation / cellular senescence / heparin binding / : / regulation of gene expression / protease binding / apoptotic process / calcium ion binding / negative regulation of apoptotic process / protein-containing complex / extracellular space / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain / Thrombospondin-5, coiled coil region / : / Cartilage oligomeric matrix protein / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain / Thrombospondin-5, coiled coil region / : / Cartilage oligomeric matrix protein / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / : / Calcium-binding EGF domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RETINOL / Cartilage oligomeric matrix protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsGuo, Y. / Bozic, D. / Malashkevich, V.N. / Kammerer, R.A. / Schulthess, T.
Citation
Journal: EMBO J. / Year: 1998
Title: All-trans retinol, vitamin D and other hydrophobic compounds bind in the axial pore of the five-stranded coiled-coil domain of cartilage oligomeric matrix protein.
Authors: Guo, Y. / Bozic, D. / Malashkevich, V.N. / Kammerer, R.A. / Schulthess, T.
#1: Journal: Proteins / Year: 1996
Title: Crystallization and Preliminary Crystallographic Study of the Pentamerizing Domain from Cartilage Oligomeric Matrix Protein: a Five-stranded Alpha-helical Bundle.
Authors: Efimov, V.P. / Engel, J. / Malashkevich, V.N.
#2: Journal: Science / Year: 1996
Title: The Crystal Structure of a Five-stranded Coiled Coil in COMP: a Prototype Ion Channel?
Authors: Malashkevich, V.N. / Kammerer, R.A. / Efimov, V.P. / Schulthess, T. / Engel, J.
History
DepositionJul 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.5Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
B: PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
C: PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
D: PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
E: PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7826
Polymers26,4965
Non-polymers2861
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-120 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.470, 49.470, 54.980
Angle α, β, γ (deg.)90.00, 103.84, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide
PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN) / COMP


Mass: 5299.129 Da / Num. of mol.: 5 / Fragment: ASSEMBLY DOMAIN
Source method: isolated from a genetically manipulated source
Details: PENTAMERIC COILED-COIL / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: CARTILAGE / Plasmid: PET-3B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P35444
#2: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.92 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: COMPcc (16 mg/ml) in 20 mM sodium phosphate, 200 mM NaCl (pH 7.5) precipitant: 7-8% PEG 8000, 50 mM sodium cacodylate (pH 6.0), 50 mM sodium acetate, 50 mM calcium acetate , VAPOR DIFFUSION, ...Details: COMPcc (16 mg/ml) in 20 mM sodium phosphate, 200 mM NaCl (pH 7.5) precipitant: 7-8% PEG 8000, 50 mM sodium cacodylate (pH 6.0), 50 mM sodium acetate, 50 mM calcium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 20.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
27-8 %PEG80001reservoir
350 mMsodium cacodylate1reservoir
450 mMsodium acetate1reservoir
550 mMcalcium acetate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→3 Å / Num. all: 5464 / Num. obs: 5464 / % possible obs: 86 % / Redundancy: 3.71 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.132
Reflection shellResolution: 2.7→3 Å / Num. unique all: 5464 / % possible all: 87.6
Reflection
*PLUS
Num. measured all: 20313
Reflection shell
*PLUS
% possible obs: 87.6 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
AMoREphasing
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.7→3 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.195 --
all0.195 5464 -
Rfree-0 -
obs-5464 87.6 %
Refinement stepCycle: LAST / Resolution: 2.7→3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 21 152 2003
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d18.68
X-RAY DIFFRACTIONx_improper_angle_d1.1
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.68
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

+
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