[English] 日本語
Yorodumi
- PDB-4bry: The Idas:Geminin heterodimeric parallel coiled-coil -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bry
TitleThe Idas:Geminin heterodimeric parallel coiled-coil
Components
  • GEMININ
  • MULTICILIN
KeywordsCELL CYCLE / DNA REPLICATION LICENSING
Function / homology
Function and homology information


multi-ciliated epithelial cell differentiation / DNA replication preinitiation complex assembly / centriole assembly / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / motile cilium assembly / regulation of cilium assembly / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / negative regulation of DNA replication ...multi-ciliated epithelial cell differentiation / DNA replication preinitiation complex assembly / centriole assembly / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / motile cilium assembly / regulation of cilium assembly / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / negative regulation of DNA replication / regulation of DNA replication / cilium assembly / negative regulation of cell cycle / Activation of the pre-replicative complex / regulation of mitotic cell cycle / transcription repressor complex / Assembly of the pre-replicative complex / animal organ morphogenesis / histone deacetylase binding / transcription corepressor activity / DNA-binding transcription factor binding / transcription coactivator activity / nuclear body / cell cycle / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Multicilin / Geminin/Multicilin / Geminin / Geminin coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Multicilin / Geminin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsCaillat, C. / Perrakis, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The Geminin and Idas Coiled Coils Preferentially Form a Heterodimer that Inhibits Geminin Function in DNA Replication Licensing
Authors: Caillate, C. / Pefani, E.D. / Gillespie, P.J. / Taraviras, S. / Blow, J.J. / Lygerou, Z. / Perrakis, A.
History
DepositionJun 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: GEMININ
B: MULTICILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3406
Polymers17,7622
Non-polymers5784
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-26 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.799, 117.799, 103.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein GEMININ /


Mass: 9376.613 Da / Num. of mol.: 1 / Fragment: COILED-COIL, RESIDUES 83-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-NKI-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O75496
#2: Protein MULTICILIN / MULTICILIATE DIFFERENTIATION AND DNA SYNTHESIS-ASSOCIATED CELL CYCLE PROTEIN / PROTEIN IDAS / IDAS


Mass: 8385.453 Da / Num. of mol.: 1 / Fragment: COILED-COIL, RESIDUES 173-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: D6RGH6
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M SPG PH 7.5, 10 % ISOPROPANOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.992
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.89→46.95 Å / Num. obs: 8415 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 81.3 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.8
Reflection shellResolution: 2.89→3.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UII

1uii


Resolution: 2.89→46.946 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU B: 21.734 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.373 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 633 7.58 %RANDOM
Rwork0.2026 ---
obs0.204 8398 99.55 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 53.113 Å2
Baniso -1Baniso -2Baniso -3
1--0.693 Å20 Å20 Å2
2---0.693 Å20 Å2
3---1.386 Å2
Refinement stepCycle: LAST / Resolution: 2.89→46.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 36 0 1175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191185
X-RAY DIFFRACTIONr_bond_other_d0.0050.02847
X-RAY DIFFRACTIONr_angle_refined_deg2.2961.9921582
X-RAY DIFFRACTIONr_angle_other_deg1.05432077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81225.87363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.66415238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.328158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021255
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
X-RAY DIFFRACTIONr_nbd_refined0.2960.2297
X-RAY DIFFRACTIONr_nbd_other0.2180.223
X-RAY DIFFRACTIONr_nbtor_refined0.2140.2530
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6064.1621183
X-RAY DIFFRACTIONr_mcbond_other1.064.332846
X-RAY DIFFRACTIONr_mcangle_it7.3856.0871582
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it12.33512.41445
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.21818.019894
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.89→2.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 45 -
Rwork0.333 491 -
obs--98.711 %
Refinement TLS params.Method: refined / Origin x: 6.7041 Å / Origin y: 25.065 Å / Origin z: -18.7028 Å
111213212223313233
T0.106 Å20.0206 Å20.013 Å2-0.2831 Å20.0421 Å2--0.0582 Å2
L9.9135 °2-0.2122 °2-1.2187 °2-0.3389 °20.1896 °2--0.3319 °2
S0.2783 Å °0.1578 Å °0.0046 Å °-0.031 Å °-0.1836 Å °-0.0527 Å °-0.0933 Å °-0.098 Å °-0.0946 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A92 - 160
2X-RAY DIFFRACTION1B176 - 244

+
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