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- PDB-3hym: Insights into Anaphase Promoting Complex TPR subdomain assembly f... -

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Basic information

Entry
Database: PDB / ID: 3hym
TitleInsights into Anaphase Promoting Complex TPR subdomain assembly from a CDC26-APC6 structure
Components
  • Anaphase-promoting complex subunit CDC26
  • Cell division cycle protein 16 homolog
KeywordsCELL CYCLE / LIGASE / APC / Anaphase Promoting Complex / Mitosis / Cyclosome / TPR / Ubiquitin / Ubiquitin Ligase / E3 / twinning / Alternative splicing / Cell division / Phosphoprotein / TPR repeat / Ubl conjugation pathway / Coiled coil / Nucleus
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 / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / 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 / CDK-mediated phosphorylation and removal of Cdc6 / mitotic spindle / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / Senescence-Associated Secretory Phenotype (SASP) / protein ubiquitination / cell division / centrosome / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Anaphase-promoting complex, subunit CDC26 / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Anaphase-promoting complex, subunit CDC26 / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / 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
Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit CDC26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsWang, J. / Dye, B.T. / Rajashankar, K.R. / Kurinov, I. / Schulman, B.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Insights into anaphase promoting complex TPR subdomain assembly from a CDC26-APC6 structure.
Authors: Wang, J. / Dye, B.T. / Rajashankar, K.R. / Kurinov, I. / Schulman, B.A.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anaphase-promoting complex subunit CDC26
B: Cell division cycle protein 16 homolog
C: Anaphase-promoting complex subunit CDC26
D: Cell division cycle protein 16 homolog
E: Anaphase-promoting complex subunit CDC26
F: Cell division cycle protein 16 homolog
G: Anaphase-promoting complex subunit CDC26
H: Cell division cycle protein 16 homolog
I: Anaphase-promoting complex subunit CDC26
J: Cell division cycle protein 16 homolog
K: Anaphase-promoting complex subunit CDC26
L: Cell division cycle protein 16 homolog


Theoretical massNumber of molelcules
Total (without water)249,11812
Polymers249,11812
Non-polymers00
Water3,801211
1
A: Anaphase-promoting complex subunit CDC26
B: Cell division cycle protein 16 homolog


Theoretical massNumber of molelcules
Total (without water)41,5202
Polymers41,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-13 kcal/mol
Surface area15160 Å2
MethodPISA
2
C: Anaphase-promoting complex subunit CDC26
D: Cell division cycle protein 16 homolog


Theoretical massNumber of molelcules
Total (without water)41,5202
Polymers41,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-18 kcal/mol
Surface area15120 Å2
MethodPISA
3
E: Anaphase-promoting complex subunit CDC26
F: Cell division cycle protein 16 homolog


Theoretical massNumber of molelcules
Total (without water)41,5202
Polymers41,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-18 kcal/mol
Surface area15480 Å2
MethodPISA
4
G: Anaphase-promoting complex subunit CDC26
H: Cell division cycle protein 16 homolog


Theoretical massNumber of molelcules
Total (without water)41,5202
Polymers41,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-18 kcal/mol
Surface area15340 Å2
MethodPISA
5
I: Anaphase-promoting complex subunit CDC26
J: Cell division cycle protein 16 homolog


Theoretical massNumber of molelcules
Total (without water)41,5202
Polymers41,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-18 kcal/mol
Surface area15250 Å2
MethodPISA
6
K: Anaphase-promoting complex subunit CDC26
L: Cell division cycle protein 16 homolog


Theoretical massNumber of molelcules
Total (without water)41,5202
Polymers41,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-18 kcal/mol
Surface area15280 Å2
MethodPISA
7
A: Anaphase-promoting complex subunit CDC26
B: Cell division cycle protein 16 homolog
E: Anaphase-promoting complex subunit CDC26
F: Cell division cycle protein 16 homolog


Theoretical massNumber of molelcules
Total (without water)83,0394
Polymers83,0394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-49 kcal/mol
Surface area28260 Å2
MethodPISA
8
C: Anaphase-promoting complex subunit CDC26
D: Cell division cycle protein 16 homolog
K: Anaphase-promoting complex subunit CDC26
L: Cell division cycle protein 16 homolog


Theoretical massNumber of molelcules
Total (without water)83,0394
Polymers83,0394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-55 kcal/mol
Surface area28190 Å2
MethodPISA
9
G: Anaphase-promoting complex subunit CDC26
H: Cell division cycle protein 16 homolog
I: Anaphase-promoting complex subunit CDC26
J: Cell division cycle protein 16 homolog


Theoretical massNumber of molelcules
Total (without water)83,0394
Polymers83,0394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-53 kcal/mol
Surface area28430 Å2
MethodPISA
10


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31960 Å2
ΔGint-184 kcal/mol
Surface area79910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)301.897, 301.897, 80.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain B and (resseq 229:347 or resseq 350:422 or resseq 444:528)
211chain D and (resseq 229:347 or resseq 350:422 or resseq 444:528)
311chain F and (resseq 229:347 or resseq 350:422 or resseq 444:528)
411chain H and (resseq 229:347 or resseq 350:422 or resseq 444:528)
511chain J and (resseq 229:347 or resseq 350:422 or resseq 444:528)
611chain L and (resseq 229:347 or resseq 350:422 or resseq 444:528)
112chain A
212chain C
312chain E
412chain G
512chain I
612chain K

NCS ensembles :
ID
1
2

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Components

#1: Protein/peptide
Anaphase-promoting complex subunit CDC26 / Cell division cycle protein 26 homolog


Mass: 3713.150 Da / Num. of mol.: 6 / Fragment: CDC26N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC26, C9orf17 / Plasmid details: pRSFDuetHISMBPAPC6TPR-CDC26N / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NHZ8
#2: Protein
Cell division cycle protein 16 homolog / CDC16Hs / Anaphase-promoting complex subunit 6 / APC6 / Cyclosome subunit 6


Mass: 37806.457 Da / Num. of mol.: 6 / Fragment: APC6TPR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC16, ANAPC6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13042
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 4.24 Å3/Da / Density % sol: 70.98 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 1:1 mix with well buffer: 0.2M MgCl2, 7% isopropanol, 0.1 M Tris-Cl pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97926 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.8→49.4 Å / Num. all: 199802 / Num. obs: 197947 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.6 / Redundancy: 5 % / Biso Wilson estimate: 65.7 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 19
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.6 / Num. unique all: 19867 / Rsym value: 0.475 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SHELXSphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→49.4 Å / Cross valid method: random / σ(F): 0.02 / Stereochemistry target values: TWIN_LSQ_F / Details: Twin operator: k, h, -l Twin fraction: 0.44
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 9730 4.92 %5%
Rwork0.1879 ---
obs0.1894 197777 98.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.278 Å2 / ksol: 0.328 e/Å3
Refinement stepCycle: LAST / Resolution: 2.8→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15306 0 0 211 15517
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2166X-RAY DIFFRACTIONPOSITIONAL
12D2166X-RAY DIFFRACTIONPOSITIONAL0.461
13F2175X-RAY DIFFRACTIONPOSITIONAL0.626
14H2162X-RAY DIFFRACTIONPOSITIONAL0.597
15J2171X-RAY DIFFRACTIONPOSITIONAL0.613
16L2153X-RAY DIFFRACTIONPOSITIONAL0.609
21A199X-RAY DIFFRACTIONPOSITIONAL
22C199X-RAY DIFFRACTIONPOSITIONAL0.568
23E203X-RAY DIFFRACTIONPOSITIONAL0.538
24G204X-RAY DIFFRACTIONPOSITIONAL0.75
25I203X-RAY DIFFRACTIONPOSITIONAL0.601
26K183X-RAY DIFFRACTIONPOSITIONAL0.557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8005-2.84880.32094400.28598446X-RAY DIFFRACTION98
2.8488-2.90050.33394560.27429048X-RAY DIFFRACTION98
2.9005-2.95630.32634700.26329197X-RAY DIFFRACTION98
2.9563-3.01670.32194640.25529242X-RAY DIFFRACTION98
3.0167-3.08230.28314850.24749405X-RAY DIFFRACTION98
3.0823-3.15390.29344760.24339282X-RAY DIFFRACTION98
3.1539-3.23280.29174860.23069481X-RAY DIFFRACTION98
3.2328-3.32020.27024820.22169522X-RAY DIFFRACTION98
3.3202-3.41790.2494790.21359476X-RAY DIFFRACTION98
3.4179-3.52820.22014830.19589518X-RAY DIFFRACTION98
3.5282-3.65420.22394910.19499571X-RAY DIFFRACTION98
3.6542-3.80050.21944860.17719595X-RAY DIFFRACTION98
3.8005-3.97340.17624880.16659571X-RAY DIFFRACTION98
3.9734-4.18280.19144820.15519538X-RAY DIFFRACTION98
4.1828-4.44470.17324900.14699608X-RAY DIFFRACTION98
4.4447-4.78760.17614890.14119471X-RAY DIFFRACTION98
4.7876-5.26890.19694920.16129541X-RAY DIFFRACTION98
5.2689-6.03010.22064890.20649585X-RAY DIFFRACTION98
6.0301-7.59290.19594870.18049562X-RAY DIFFRACTION98
7.5929-49.41720.16774960.15249507X-RAY DIFFRACTION98
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)
10.0288-0.0612-0.02250.1036-0.01540.0349-0.09030.06440.11330.09220.15110.0903-0.0715-0.0426-0.04580.08760.2521-0.0139-0.23530.1956-0.1428-87.469-102.3084-23.5773
20.0516-0.0162-0.0531-0.00850.02320.03420.04620.01330.03960.01470.0035-0.0702-0.07340.1092-0.0471-0.06340.14990.32810.13740.0185-0.1383-76.2797-119.7765-1.935
3-0.04310.02830.0086-0.14590.05040.0259-0.18460.00810.06240.0215-0.08380.02960.17670.1346-0.33480.05290.3252-0.1165-0.2720.35830.2133-87.4402-73.2947-6.5783
40.1952-0.01940.22340.0093-0.030.23260.00260.12720.00020.0566-0.0905-0.0318-0.04870.28770.1274-0.1922-0.0908-0.38570.31080.49180.4714-75.4882-56.2151-28.126
50.18580.15720.12230.22390.27230.25450.06930.0973-0.0760.16090.0778-0.07820.08530.01770.2126-0.1134-0.0236-0.12290.2304-0.1443-0.187-43.532-128.5834-7.9323
60.0614-0.01510.02940.03860.0690.46360.04350.1274-0.03960.00560.1013-0.0329-0.12340.19390.3404-0.01540.02190.05370.16-0.1029-0.34-62.8019-125.3845-30.8117
7-0.00980.00360.0325-0.0362-0.03030.0474-0.0739-0.0266-0.09920.0425-0.0204-0.13590.03-0.2071-0.1715-0.3529-0.0931-0.42640.3043-0.27060.211-16.7355-113.2311-22.0816
80.0311-0.01520.00360.0095-0.03040.024-0.12050.0091-0.00260.12510.0193-0.1334-0.2089-0.07680.02190.30180.317-0.56830.0119-0.12870.2962-9.352-95.56261.138
90.08520.05460.01240.40910.08150.25830.15760.1224-0.08220.3650.2866-0.32730.12060.10570.78820.03460.4941-0.40750.0807-0.0281-0.056-17.2208-62.1656-5.6335
100.01890.06180.11090.11260.05650.22560.016-0.05460.1381-0.0350.3384-0.26740.08130.03280.1014-0.2067-0.1793-0.0460.3173-0.45910.6029-8.5327-79.9247-28.3425
110.30690.0476-0.10210.3273-0.01840.1429-0.09530.14580.08630.12930.48930.32630.0132-0.17660.3291-0.22220.3186-0.09310.2340.43830.1641-43.1883-47.3509-21.108
120.0739-0.0465-0.01270.1373-0.07210.10870.18030.13610.18560.03820.0297-0.0132-0.0701-0.13890.24040.11980.39070.08550.070.11610.35-62.9398-50.19511.7209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain B and resid 229:421)
2X-RAY DIFFRACTION2chain B and resid 422:529)
3X-RAY DIFFRACTION3chain D and resid 229:421)
4X-RAY DIFFRACTION4chain D and resid 422:529)
5X-RAY DIFFRACTION5chain F and resid 229:421)
6X-RAY DIFFRACTION6chain F and resid 422:529)
7X-RAY DIFFRACTION7chain H and resid 229:421)
8X-RAY DIFFRACTION8chain H and resid 422:529)
9X-RAY DIFFRACTION9chain J and resid 229:421)
10X-RAY DIFFRACTION10chain J and resid 422:529)
11X-RAY DIFFRACTION11chain L and resid 229:421)
12X-RAY DIFFRACTION12chain L and resid 422:529)

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