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- PDB-3t1n: Structure of human MICROCEPHALIN (MCPH1) TANDEM BRCT domains in c... -

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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 / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / neuronal stem cell population maintenance ...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 / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / neuronal stem cell population maintenance / Phosphorylation of the APC/C / regulation of centrosome cycle / protein K11-linked ubiquitination / protein localization to centrosome / regulation of mitotic cell cycle / establishment of mitotic spindle orientation / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / 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 / bone development / mitotic spindle / cerebral cortex development / spindle / CDK-mediated phosphorylation and removal of Cdc6 / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / regulation of inflammatory response / Senescence-Associated Secretory Phenotype (SASP) / 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, a BRCA1 C-terminus domain / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat ...Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / Anaphase-promoting complex, cyclosome, subunit 3 / BRCT domain / BRCT domain, a BRCA1 C-terminus domain / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / breast cancer carboxy-terminal domain / TPR repeat region circular profile. / TPR repeat profile. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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