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- PDB-2xpi: Crystal structure of APC/C hetero-tetramer Cut9-Hcn1 -

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Basic information

Entry
Database: PDB / ID: 2xpi
TitleCrystal structure of APC/C hetero-tetramer Cut9-Hcn1
Components
  • ANAPHASE-PROMOTING COMPLEX SUBUNIT CUT9
  • ANAPHASE-PROMOTING COMPLEX SUBUNIT HCN1 HCN1/CDC26,20S CYCLOSOME/APC COMPLEX PROTEIN HCN1, CHAPERONE-LIKE PROTEIN HCN1, HIGH COPY SUPPRESSOR OF CUT9 PROTEIN 1
KeywordsCELL CYCLE / TPR / UBIQUITIN LIGASE / E3 / CELL DIVISION / N-ACETYLATION
Function / homology
Function and homology information


: / Inactivation of APC/C via direct inhibition of the APC/C complex / : / : / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / : / Separation of Sister Chromatids / Regulation of APC/C activators between G1/S and early anaphase / : / pericentric heterochromatin => GO:0005721 ...: / Inactivation of APC/C via direct inhibition of the APC/C complex / : / : / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / : / Separation of Sister Chromatids / Regulation of APC/C activators between G1/S and early anaphase / : / pericentric heterochromatin => GO:0005721 / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of exit from mitosis / anaphase-promoting complex / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / metaphase/anaphase transition of mitotic cell cycle / regulation of mitotic metaphase/anaphase transition / protein ubiquitination / cell division / nucleus / cytosol / cytoplasm
Similarity search - Function
Anaphase-promoting complex, subunit CDC26 / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex, cyclosome, subunit 3 / : / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...Anaphase-promoting complex, subunit CDC26 / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex, cyclosome, subunit 3 / : / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
GOLD (I) CYANIDE ION / Anaphase-promoting complex subunit hcn1 / Anaphase-promoting complex subunit cut9
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsZhang, Z. / Kulkarni, K.A. / Barford, D.
CitationJournal: Embo J. / Year: 2010
Title: The Apc/C Subunit Cdc16/Cut9 is a Contiguous Tetratricopeptide Superhelix with a Homo-Dimer Interface Similar to Cdc27
Authors: Zhang, Z. / Kulkarni, K.A. / Hanrahan, S.J. / Thompson, A.J. / Barford, D.
History
DepositionAug 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Other / Version format compliance
Revision 1.2Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANAPHASE-PROMOTING COMPLEX SUBUNIT CUT9
B: ANAPHASE-PROMOTING COMPLEX SUBUNIT HCN1 HCN1/CDC26,20S CYCLOSOME/APC COMPLEX PROTEIN HCN1, CHAPERONE-LIKE PROTEIN HCN1, HIGH COPY SUPPRESSOR OF CUT9 PROTEIN 1
D: ANAPHASE-PROMOTING COMPLEX SUBUNIT CUT9
E: ANAPHASE-PROMOTING COMPLEX SUBUNIT HCN1 HCN1/CDC26,20S CYCLOSOME/APC COMPLEX PROTEIN HCN1, CHAPERONE-LIKE PROTEIN HCN1, HIGH COPY SUPPRESSOR OF CUT9 PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,3278
Polymers153,3314
Non-polymers9964
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-109.2 kcal/mol
Surface area44080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.400, 151.920, 91.870
Angle α, β, γ (deg.)90.00, 90.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT CUT9 / / CUT9/CDC16 / 20S CYCLOSOME/APC COMPLEX PROTEIN CUT9 / CELL UNTIMELY TORN PROTEIN 9


Mass: 67552.539 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-597
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Plasmid: PFBDM / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P41889
#2: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT HCN1 HCN1/CDC26,20S CYCLOSOME/APC COMPLEX PROTEIN HCN1, CHAPERONE-LIKE PROTEIN HCN1, HIGH COPY SUPPRESSOR OF CUT9 PROTEIN 1 /


Mass: 9113.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Plasmid: PFBDM / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: O13916
#3: Chemical
ChemComp-AUC / GOLD (I) CYANIDE ION


Mass: 249.001 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2AuN2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBREAKS IN THE POLYPEPTIDE OCCUR IN THE RESIDUE RANGE 61-82 AND 181-191.

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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: 2.49 Å3/Da / Density % sol: 50.56 % / Description: NONE
Crystal growpH: 7.5
Details: 100 MM HEPES (PH 7.5), 100 MM SODIUM ACETATE, 12.5% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0397
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0397 Å / Relative weight: 1
ReflectionResolution: 2.6→78.61 Å / Num. obs: 45418 / % possible obs: 99.2 % / Observed criterion σ(I): 1.5 / Redundancy: 5.5 % / Biso Wilson estimate: 55.25 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.5 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→54.394 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 1576 3.5 %
Rwork0.1887 --
obs0.1908 45376 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.189 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2935 Å20 Å2-6.6707 Å2
2---0.1627 Å20 Å2
3----4.1308 Å2
Refinement stepCycle: LAST / Resolution: 2.6→54.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8626 0 4 49 8679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018807
X-RAY DIFFRACTIONf_angle_d1.24711946
X-RAY DIFFRACTIONf_dihedral_angle_d21.4323116
X-RAY DIFFRACTIONf_chiral_restr0.0871350
X-RAY DIFFRACTIONf_plane_restr0.0041512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.68390.31061380.27753764X-RAY DIFFRACTION94
2.6839-2.77980.32771490.23973963X-RAY DIFFRACTION100
2.7798-2.89110.28011270.21094019X-RAY DIFFRACTION100
2.8911-3.02270.26151340.20094025X-RAY DIFFRACTION100
3.0227-3.18210.27071470.20254008X-RAY DIFFRACTION100
3.1821-3.38140.28361400.1994007X-RAY DIFFRACTION100
3.3814-3.64240.26051270.18734037X-RAY DIFFRACTION100
3.6424-4.00890.24151370.16674007X-RAY DIFFRACTION100
4.0089-4.58870.18391530.14184029X-RAY DIFFRACTION100
4.5887-5.78030.24221620.16353983X-RAY DIFFRACTION99
5.7803-54.4060.22471620.19213958X-RAY DIFFRACTION97
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)
10.9396-0.85071.62260.7976-0.78766.1489-0.0322-0.02350.04730.1606-0.078-0.0416-0.58820.08330.10750.2713-0.03690.01920.306-0.03580.327.851970.7215137.2324
21.9771-0.4708-0.08282.24791.00393.1663-0.01080.5528-0.148-0.3118-0.0411-0.0846-0.45070.11740.05510.1490.00360.03080.37340.01260.188624.260466.4509113.2457
35.91071.2815-2.44734.2843-2.64072.19140.2230.6073-0.0302-0.8491-0.17260.07860.7160.1751-0.07420.52250.1302-0.11950.675-0.08110.454720.684452.2286100.2139
40.34130.63650.31330.32990.12652.26230.35860.2609-0.1595-0.03670.074-0.0610.26660.6586-0.32980.08750.10620.00420.3089-0.16190.396520.450241.7877110.3491
55.1626-0.2926-1.73410.85180.02610.7170.2077-0.8241-0.68760.2963-0.4115-0.06790.37440.03060.13410.40970.022-0.03120.66460.08730.59613.693539.7799120.3146
60.5324-0.19190.20512.44420.72212.0779-0.0762-0.1803-0.0045-0.08020.10540.4398-0.2224-0.3777-0.00640.06840.05150.05580.3543-0.00850.2496-1.251850.7279109.4393
71.59980.37341.11422.95990.70882.4133-0.14020.1426-0.1654-0.82070.2351-0.05910.09150.0825-0.08850.4576-0.07450.04540.2651-0.01860.32050.869440.298987.4081
80.5552-0.4790.04761.511-0.08740.9957-0.1918-0.16960.0491-0.02690.51690.42470.1021-0.3989-0.27410.4586-0.0811-0.12430.32830.12820.4908-17.872427.278685.7494
90.24810.27020.1871.2760.40443.67120.08450.1753-0.20690.1385-0.031-0.23570.18790.3282-0.06750.14450.02140.01260.3708-0.02740.303831.634952.127737.4091
101.9827-0.00161.19680.64761.13193.69970.2622-0.4062-0.54810.66050.063-0.24331.06930.0565-0.25490.63110.0011-0.02970.37360.01940.449126.307945.838354.4955
118.212.6906-6.86765.3507-3.93256.4017-0.1359-0.971-0.37171.45780.28450.7270.0977-0.477-0.090.6215-0.02690.20030.46930.02140.424318.452847.125567.0121
121.9990.6417-0.15772.3316-0.43290.71410.0043-0.82720.12950.87780.02180.041-0.2210.3968-0.04050.66590.0427-0.03050.6658-0.05240.341130.923465.105268.6639
130.60530.722-0.37070.7744-0.34410.87940.1891-0.06690.0494-0.06290.01650.2396-0.5546-0.005-0.12060.64140.0791-0.03710.3722-0.0320.413314.997380.988266.9113
142.78410.75370.07253.955-0.48260.3533-0.25490.5723-0.0648-0.30370.1394-0.00490.1278-0.27170.06920.32970.0013-0.0880.3129-0.05740.14541.65570.477371.0739
151.443-0.2595-1.03360.67520.95953.0084-0.0531-0.1018-0.03660.37040.0284-0.17590.00250.01730.03170.56270.0525-0.07310.2341-0.01550.34538.867380.115494.2461
160.3964-0.1537-1.03592.59711.14644.74740.1130.23560.23740.01220.13540.5167-0-1.0255-0.28530.57320.09230.12320.58350.05530.6756-9.693491.588100.7923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 43:166)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 167:278)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 279:284)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 285:349)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 350:372)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 373:444)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 445:544)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 545:595)
9X-RAY DIFFRACTION9(CHAIN D AND RESID 43:144)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 145:211)
11X-RAY DIFFRACTION11(CHAIN D AND RESID 212:222)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 223:305)
13X-RAY DIFFRACTION13(CHAIN D AND RESID 306:359)
14X-RAY DIFFRACTION14(CHAIN D AND RESID 360:454)
15X-RAY DIFFRACTION15(CHAIN D AND RESID 455:545)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 546:595)

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