[English] 日本語
Yorodumi
- PDB-3t1n: Structure of human MICROCEPHALIN (MCPH1) TANDEM BRCT domains in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t1n
TitleStructure of human MICROCEPHALIN (MCPH1) TANDEM BRCT domains in complex with a CDC27 phosphopeptide
Components
  • Cdc27 peptide
  • Microcephalin
KeywordsCELL CYCLE/Peptide / Tandem BRCT domains / Cell cycle regulation / DNA repair / mitosis / Phosphorylation / CELL CYCLE-Peptide complex
Function / homology
Function and homology information


regulation of chromosome condensation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / protein branched polyubiquitination / metaphase/anaphase transition of mitotic cell cycle / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process ...regulation of chromosome condensation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / protein branched polyubiquitination / metaphase/anaphase transition of mitotic cell cycle / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / neuronal stem cell population maintenance / Phosphorylation of the APC/C / regulation of centrosome cycle / protein K11-linked ubiquitination / protein localization to centrosome / Regulation of APC/C activators between G1/S and early anaphase / establishment of mitotic spindle orientation / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / cerebral cortex development / bone development / CDK-mediated phosphorylation and removal of Cdc6 / spindle / neuron projection development / mitotic spindle / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / Senescence-Associated Secretory Phenotype (SASP) / regulation of inflammatory response / protein phosphatase binding / protein ubiquitination / cell division / centrosome / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / Anaphase-promoting complex, cyclosome, subunit 3 / BRCT domain / BRCT domain / Tetratricopeptide repeat / Tetratricopeptide repeat / breast cancer carboxy-terminal domain ...Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / Anaphase-promoting complex, cyclosome, subunit 3 / BRCT domain / BRCT domain / Tetratricopeptide repeat / Tetratricopeptide repeat / breast cancer carboxy-terminal domain / BRCT domain profile. / TPR repeat region circular profile. / BRCT domain / BRCT domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division cycle protein 27 homolog / Microcephalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSingh, N. / Thompson, J.R. / Mer, G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Molecular Basis for the Association of Microcephalin (MCPH1) Protein with the Cell Division Cycle Protein 27 (Cdc27) Subunit of the Anaphase-promoting Complex.
Authors: Singh, N. / Wiltshire, T.D. / Thompson, J.R. / Mer, G. / Couch, F.J.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microcephalin
B: Microcephalin
C: Cdc27 peptide
D: Cdc27 peptide


Theoretical massNumber of molelcules
Total (without water)45,0524
Polymers45,0524
Non-polymers00
Water1,18966
1
A: Microcephalin
C: Cdc27 peptide


Theoretical massNumber of molelcules
Total (without water)22,5262
Polymers22,5262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-7 kcal/mol
Surface area10040 Å2
MethodPISA
2
B: Microcephalin
D: Cdc27 peptide


Theoretical massNumber of molelcules
Total (without water)22,5262
Polymers22,5262
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-8 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.201, 46.506, 55.322
Angle α, β, γ (deg.)86.06, 70.69, 89.67
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Microcephalin


Mass: 21949.551 Da / Num. of mol.: 2
Fragment: C-TERMINAL TANDEM BRCT DOMAINS, UNP RESIDUES 640-835
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCPH1 / Plasmid: PTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 ROSETTA (DE3) / References: UniProt: Q8NEM0
#2: Protein/peptide Cdc27 peptide


Mass: 576.447 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic peptide corresponding to the last four residues of human Cdc27 (Ser821 to Phe824). Ser821 is phosphorylated.
Source: (synth.) Homo sapiens (human) / References: UniProt: P30260*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 30% PEG 3350, 0.3 M NACL, 0.1 M BIS-TRIS, PH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→28.71 Å / Num. obs: 10161 / % possible obs: 92.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.29 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T29

1t29


Resolution: 2.6→28.71 Å / SU ML: 0.94 / σ(F): 1.97 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 487 4.8 %RANDOM
Rwork0.2307 ---
obs0.2322 10145 92.03 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.767 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.2171 Å21.9508 Å23.6261 Å2
2---2.5597 Å21.058 Å2
3----3.6574 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 0 66 3081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023131
X-RAY DIFFRACTIONf_angle_d0.6694278
X-RAY DIFFRACTIONf_dihedral_angle_d12.4691147
X-RAY DIFFRACTIONf_chiral_restr0.038488
X-RAY DIFFRACTIONf_plane_restr0.003536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.9760.32191740.30813331X-RAY DIFFRACTION95
2.976-3.74810.28351620.25213015X-RAY DIFFRACTION86
3.7481-28.71120.2281510.19383312X-RAY DIFFRACTION95
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)
10.8042-0.0775-0.79532.6761-0.90571.1842-0.1508-0.06930.065-0.1630.22510.3705-0.2627-0.2207-0.05520.56790.13860.0130.27330.04450.2379-7.17535.36893.8237
24.68920.08520.75393.0710.74973.6792-0.22250.1098-1.1079-0.03610.77960.7280.0033-0.4924-0.28750.2724-0.00360.05810.19850.03880.4752-13.240311.82818.7482
31.769-1.29980.92021.1606-0.67262.16460.0028-0.1550.11690.30560.11930.02850.2502-0.0307-0.1470.25110.0157-0.00890.2333-0.06010.2305-1.30321.98226.0607
41.87750.4598-0.20691.29790.9592.23770.1106-0.04570.16560.27230.13620.1807-0.2695-0.0234-0.16270.2448-0.03870.09070.2466-0.03910.3593-1.32516.61368.0519
52.2459-0.5979-1.55432.27270.82213.69280.2925-0.2390.2728-0.29880.0569-0.09670.05880.1954-0.31530.26330.01370.02830.3085-0.04730.275610.38416.38867.7585
61.09670.25460.11592.39450.45631.4529-0.06460.095-0.0305-0.4350.06820.1343-0.02390.021-0.01640.28870.0284-0.01790.2476-0.06850.250910.1285-14.05552.9095
74.1942.7363-1.33762.0658-1.26280.9842-0.02960.2989-0.3340.73930.1111-0.11260.3487-0.40910.09680.53410.06210.24050.4684-0.01920.468413.7043-27.708812.4195
81.43831.87810.36414.8141-0.89522.0396-1.0625-0.3660.49320.35960.5299-1.2049-0.3248-0.19980.06670.4577-0.00080.06310.2534-0.03860.087312.9265-11.48313.1759
91.49380.5024-0.07141.9132-1.26532.33590.0852-0.1286-0.20150.4193-0.6082-0.49041.1721-0.41970.08820.29660.2189-0.16720.5852-0.05230.298917.9524-11.542515.1333
100.5706-0.3610.28891.8039-0.34196.6550.1978-0.4468-0.20610.01190.2523-0.1152-0.7966-0.0476-0.12830.3175-0.00830.0150.403-0.0690.377720.119524.9381-15.6809
112.9129-0.5629-0.14642.50320.67963.8065-0.54030.63720.0251-0.35640.937-1.0179-0.36321.2105-0.31490.4299-0.11440.00360.34030.05120.593326.420431.0238-19.8222
121.8190.28390.61131.37510.9622.27410.10970.1875-0.1282-0.05710.0021-0.11980.03180.09-0.12710.277-0.0067-0.02640.22950.00410.302116.477622.703-16.8787
130.7452-0.5384-0.211.3885-0.93311.03050.1926-0.05260.1522-0.1506-0.2898-0.12640.19650.10810.04120.27990.03640.02990.204-0.01640.324212.161630.5741-19.3484
141.06611.6906-0.27082.64410.95712.03550.152-0.1144-0.00420.5424-0.1230.166-0.06130.0626-0.05790.2287-0.0380.02740.299-0.02540.24462.91059.8102-13.3043
155.8586-3.6319-2.44912.16961.86164.96080.5380.7806-0.24460.4585-1.0831-0.02330.69260.03410.03650.3774-0.16720.14560.195-0.24260.5003-0.4309-6.9203-22.6587
161.04550.74010.23252.63840.59321.493-0.02050.7011-0.20510.0456-0.09130.2274-0.20440.05130.17470.3582-0.0641-0.0130.4486-0.02020.2407-1.83377.2677-24.9714
175.7134-3.9662.84462.702-1.9511.4212-0.3962-0.3890.18060.523-0.2781-0.1371-0.0703-0.20680.07670.48530.160.05020.48020.03690.4206-1.5233-5.656916.5744
180.65561.1892-0.0772.2054-0.1215-0.0458-0.61060.42310.4125-0.57380.562-0.2218-0.13830.1867-0.03830.34790.06890.06280.36830.09180.394314.633213.5482-27.6766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 644:656)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 657:670)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 671:705)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 706:728)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 729:745)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 746:797)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 798:808)A0
8X-RAY DIFFRACTION8chain 'A' and (resseq 809:822)A0
9X-RAY DIFFRACTION9chain 'A' and (resseq 823:834)A0
10X-RAY DIFFRACTION10chain 'B' and (resseq 645:656)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 657:670)B0
12X-RAY DIFFRACTION12chain 'B' and (resseq 671:694)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 695:734)B0
14X-RAY DIFFRACTION14chain 'B' and (resseq 735:794)B0
15X-RAY DIFFRACTION15chain 'B' and (resseq 795:808)B0
16X-RAY DIFFRACTION16chain 'B' and (resseq 809:834)B0
17X-RAY DIFFRACTION17chain 'C'C0
18X-RAY DIFFRACTION18chain 'D'D0

+
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