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- PDB-3ffl: Crystal Structure of the N-terminal Domain of Anaphase-Promoting ... -

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Basic information

Entry
Database: PDB / ID: 3ffl
TitleCrystal Structure of the N-terminal Domain of Anaphase-Promoting Complex Subunit 7
ComponentsAnaphase-promoting complex subunit 7
KeywordsCELL CYCLE / Tetratricopeptide repeat motif / helis-turn-helix / Cell division / Mitosis / TPR repeat / Ubl conjugation pathway
Function / homology
Function and homology information


Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / protein branched polyubiquitination / 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 / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / positive regulation of mitotic metaphase/anaphase transition ...Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / protein branched polyubiquitination / 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 / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / positive regulation of mitotic metaphase/anaphase transition / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / heterochromatin / regulation of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / 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 / brain development / CDK-mediated phosphorylation and removal of Cdc6 / spindle / Separation of Sister Chromatids / microtubule cytoskeleton / Antigen processing: Ubiquitination & Proteasome degradation / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / protein ubiquitination / cell division / nucleoplasm / nucleus / cytosol
Similarity search - Function
Tetratricopeptide repeat / 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
Anaphase-promoting complex subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHan, D. / Kim, K. / Kim, Y. / Kim, Y.
CitationJournal: To be published
Title: Crystal Structure of the N-terminal Domain of Anaphase-Promoting Complex Subunit 7
Authors: Han, D. / Kim, K. / Kim, Y. / Kang, Y. / Kim, Y.
History
DepositionDec 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Refinement description
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anaphase-promoting complex subunit 7
B: Anaphase-promoting complex subunit 7
C: Anaphase-promoting complex subunit 7
D: Anaphase-promoting complex subunit 7


Theoretical massNumber of molelcules
Total (without water)74,8584
Polymers74,8584
Non-polymers00
Water86548
1
A: Anaphase-promoting complex subunit 7
C: Anaphase-promoting complex subunit 7


Theoretical massNumber of molelcules
Total (without water)37,4292
Polymers37,4292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-13 kcal/mol
Surface area13980 Å2
MethodPISA
2
B: Anaphase-promoting complex subunit 7
D: Anaphase-promoting complex subunit 7


Theoretical massNumber of molelcules
Total (without water)37,4292
Polymers37,4292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-14 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.493, 64.076, 81.597
Angle α, β, γ (deg.)90.00, 95.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Anaphase-promoting complex subunit 7 / APC7 / Cyclosome subunit 7


Mass: 18714.484 Da / Num. of mol.: 4 / Fragment: N-terminal domain / Mutation: M49L, M128L, M134V, M160L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC7, APC7 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9UJX3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M sodium/potassium tartrate, 15% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDCrystal-ID
11
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A10.97950, 0.97956, 0.97171
SYNCHROTRONPAL/PLS 6B20.97950, 0.97956, 0.97171
SYNCHROTRONPAL/PLS 6C130.97950, 0.97956, 0.97171
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 2, 2008
ADSC QUANTUM 2102CCDOct 15, 2007
ADSC QUANTUM 2103CCDMar 16, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
3MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979561
30.971711
ReflectionResolution: 2.5→41.5 Å / Num. obs: 24411 / % possible obs: 100 %
Reflection shellResolution: 2.5→2.565 Å / Num. unique all: 1214 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→41 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 23.89 / SU ML: 0.235 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24012 1300 5.1 %RANDOM
Rwork0.21647 ---
obs0.21768 24411 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.414 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0.08 Å2
2---0.82 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 0 0 48 4045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0224065
X-RAY DIFFRACTIONr_angle_refined_deg0.8221.9915493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1345492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70724.773176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.20415769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.971520
X-RAY DIFFRACTIONr_chiral_restr0.050.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212956
X-RAY DIFFRACTIONr_mcbond_it0.1831.52508
X-RAY DIFFRACTIONr_mcangle_it0.35924048
X-RAY DIFFRACTIONr_scbond_it0.52831557
X-RAY DIFFRACTIONr_scangle_it0.8934.51445
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 59 -
Rwork0.339 1214 -
obs--100 %
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)
14.0892-0.52913.17795.12892.631114.54930.26380.4809-0.4342-0.90520.1139-0.15130.56550.0455-0.37780.56190.034-0.08370.3687-0.03410.12445.426-0.593-38.298
25.76730.42442.9088.65883.66515.31820.19090.0230.0016-0.7621-0.0303-0.11120.1798-0.2724-0.16060.2575-0.0186-0.03970.35110.02970.10186.474.263-25.453
36.79491.66633.53394.78812.099913.3654-0.0531-0.53280.4283-0.3747-0.027-0.1171-0.9826-0.0230.08010.19870.0007-0.00530.3487-0.05050.149411.29211.549-15.066
46.9284-2.1781-0.99968.9672.43615.3574-0.237-0.5814-0.2490.75030.4238-1.57270.45680.5028-0.18680.05030.0293-0.23590.73690.00850.572528.641-1.9012.978
58.3939-1.64890.22914.1711-0.11668.6141-0.0863-0.6752-0.19890.31930.0862-0.547-0.08390.05610.0001-0.015-0.0341-0.1230.5908-0.01450.131215.0413.6112.891
69.94730.72432.12165.94091.721510.04230.0313-0.59850.56640.37020.0335-0.0962-0.73790.072-0.06480.1359-0.0074-0.05560.6088-0.12670.12014.59210.7149.165
76.16350.65632.87684.5960.499611.43480.02290.6737-0.0295-1.11560.1506-0.13030.0940.7998-0.17350.4627-0.01910.01270.64270.09180.130411.58133.203-29.389
88.1709-1.32622.27247.41341.006110.71040.11570.34620.0358-0.5923-0.0193-0.36430.14330.6497-0.09640.1976-0.03960.00330.51920.10620.099412.54434.059-17.352
99.81730.42132.97514.87620.91388.1403-0.1981-0.28590.53910.00580.0888-0.3152-0.37570.42810.10930.1131-0.0491-0.04580.64490.05820.229317.3538.708-4.612
1016.160.8593.880811.0135-1.08617.9074-0.6505-1.32291.71741.3141-0.3577-2.7985-0.2945-0.20641.00820.2055-0.0339-0.32040.8692-0.15911.005142.06930.4778.418
1110.0425-2.79631.23218.3997-1.60994.0383-0.339-0.6686-0.48560.6390.647-0.46790.1444-0.5938-0.3080.01850.0163-0.1240.6985-0.01880.168529.36223.3068.151
1216.4661-2.15383.51396.1698-8.498713.1356-0.6202-3.30310.30352.77911.58631.2105-0.8584-1.6525-0.96610.73240.65670.37832.15320.34460.188216.72127.60421.831
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 74
2X-RAY DIFFRACTION2A75 - 133
3X-RAY DIFFRACTION3A134 - 166
4X-RAY DIFFRACTION4B21 - 72
5X-RAY DIFFRACTION5B73 - 136
6X-RAY DIFFRACTION6B137 - 166
7X-RAY DIFFRACTION7C22 - 68
8X-RAY DIFFRACTION8C69 - 124
9X-RAY DIFFRACTION9C125 - 166
10X-RAY DIFFRACTION10D22 - 41
11X-RAY DIFFRACTION11D42 - 142
12X-RAY DIFFRACTION12D143 - 165

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