[English] 日本語
Yorodumi
- PDB-5czo: Structure of S. cerevisiae Hrr25:Mam1 complex, form 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5czo
TitleStructure of S. cerevisiae Hrr25:Mam1 complex, form 2
Components
  • Casein kinase I homolog HRR25
  • Monopolin complex subunit MAM1
KeywordsTRANSFERASE / casein kinase / monopolin
Function / homology
Function and homology information


meiotic sister chromatid cohesion involved in meiosis I / regulation of vesicle fusion with Golgi apparatus / regulation of protein localization by the Cvt pathway / monopolin complex / positive regulation of clathrin-dependent endocytosis / spindle attachment to meiosis I kinetochore / meiotic chromosome segregation / regulation of ER to Golgi vesicle-mediated transport / COPII-mediated vesicle transport / tRNA wobble uridine modification ...meiotic sister chromatid cohesion involved in meiosis I / regulation of vesicle fusion with Golgi apparatus / regulation of protein localization by the Cvt pathway / monopolin complex / positive regulation of clathrin-dependent endocytosis / spindle attachment to meiosis I kinetochore / meiotic chromosome segregation / regulation of ER to Golgi vesicle-mediated transport / COPII-mediated vesicle transport / tRNA wobble uridine modification / cellular bud tip / homologous chromosome segregation / cellular bud neck / regulation of autophagosome assembly / pexophagy / spindle pole body / preribosome, small subunit precursor / chromosome, centromeric region / regulation of DNA repair / ribosomal large subunit biogenesis / P-body / kinetochore / endocytosis / regulation of protein localization / ribosomal small subunit biogenesis / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Monopolin complex, subunit Mam1 / Monopolin complex protein MAM1 / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...Monopolin complex, subunit Mam1 / Monopolin complex protein MAM1 / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Casein kinase I homolog HRR25 / Monopolin complex subunit MAM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.894 Å
AuthorsYe, Q. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104141 United States
CitationJournal: Embo J. / Year: 2016
Title: Structure of the Saccharomyces cerevisiae Hrr25:Mam1 monopolin subcomplex reveals a novel kinase regulator.
Authors: Ye, Q. / Ur, S.N. / Su, T.Y. / Corbett, K.D.
History
DepositionJul 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase I homolog HRR25
C: Monopolin complex subunit MAM1
B: Casein kinase I homolog HRR25
D: Monopolin complex subunit MAM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3826
Polymers118,2514
Non-polymers1312
Water70339
1
A: Casein kinase I homolog HRR25
C: Monopolin complex subunit MAM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1913
Polymers59,1262
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-25 kcal/mol
Surface area22460 Å2
MethodPISA
2
B: Casein kinase I homolog HRR25
D: Monopolin complex subunit MAM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1913
Polymers59,1262
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-22 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.701, 83.841, 132.508
Angle α, β, γ (deg.)90.00, 92.57, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Casein kinase I homolog HRR25


Mass: 46249.059 Da / Num. of mol.: 2 / Mutation: K38R
Source method: isolated from a genetically manipulated source
Details: surface LYS residues methylated (MLY)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HRR25, YPL204W / Production host: Escherichia coli (E. coli)
References: UniProt: P29295, non-specific serine/threonine protein kinase
#2: Protein Monopolin complex subunit MAM1 / Monopolar microtubule attachment during meiosis 1 protein 1


Mass: 12876.634 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: surface LYS residues methylated (MLY)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MAM1, YER106W / Production host: Escherichia coli (E. coli) / References: UniProt: P40065
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Imidazole pH 8.0, 14% PEG3350, 6% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.2829 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2829 Å / Relative weight: 1
ReflectionResolution: 2.89→132.4 Å / % possible obs: 99.8 % / Redundancy: 3.5 % / Rsym value: 0.112 / Net I/σ(I): 15.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.36 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHL

4xhl


Resolution: 2.894→49.692 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 30.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 2572 5.12 %
Rwork0.2178 --
obs0.2197 50244 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.894→49.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7917 0 2 39 7958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028100
X-RAY DIFFRACTIONf_angle_d0.50510883
X-RAY DIFFRACTIONf_dihedral_angle_d12.4283083
X-RAY DIFFRACTIONf_chiral_restr0.0231133
X-RAY DIFFRACTIONf_plane_restr0.0021386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8942-2.94980.44521150.35392432X-RAY DIFFRACTION90
2.9498-3.010.39171450.33722675X-RAY DIFFRACTION100
3.01-3.07550.44311460.34192680X-RAY DIFFRACTION100
3.0755-3.1470.34021460.32172647X-RAY DIFFRACTION100
3.147-3.22570.3851340.32582640X-RAY DIFFRACTION100
3.2257-3.31290.39121380.30372723X-RAY DIFFRACTION100
3.3129-3.41040.34451130.2742650X-RAY DIFFRACTION100
3.4104-3.52040.28681260.25242721X-RAY DIFFRACTION100
3.5204-3.64620.25191690.23252603X-RAY DIFFRACTION100
3.6462-3.79210.30711520.22132670X-RAY DIFFRACTION100
3.7921-3.96470.24511520.20392648X-RAY DIFFRACTION100
3.9647-4.17360.20561340.18412642X-RAY DIFFRACTION100
4.1736-4.43490.19741350.17642692X-RAY DIFFRACTION100
4.4349-4.77710.18881690.15442664X-RAY DIFFRACTION100
4.7771-5.25730.20951440.18652665X-RAY DIFFRACTION100
5.2573-6.0170.26381560.21052610X-RAY DIFFRACTION100
6.017-7.57640.24731410.22672695X-RAY DIFFRACTION100
7.5764-49.69930.20761570.18042615X-RAY DIFFRACTION99
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)
11.8182-0.14160.12282.3594-0.11792.7223-0.1552-0.1577-0.05430.2254-0.01550.40670.009-0.35960.14390.35210.05350.060.4371-0.00620.5389-35.5127-0.163711.6359
22.4693-0.63291.15552.9451-0.85233.4739-0.0948-0.11580.26560.0349-0.0714-0.05610.0826-0.20260.11050.3835-0.01770.02670.47990.01050.4033-12.706-10.445455.639
32.4284-0.69450.67762.6145-1.2664.0624-0.04380.2487-0.1767-0.51210.06150.5576-0.0546-0.2334-0.0280.6242-0.0342-0.1630.5114-0.03550.8167-38.126-7.5072-9.8443
41.41060.28010.77523.4628-1.09893.1248-0.1449-0.70770.3560.92740.13750.373-0.2027-0.39680.00680.85090.1521-0.02450.8886-0.20680.6251-14.1413-4.771177.4115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain C
4X-RAY DIFFRACTION4Chain D

+
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