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- PDB-4r2y: Crystal structure of APC11 RING domain -

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Basic information

Entry
Database: PDB / ID: 4r2y
TitleCrystal structure of APC11 RING domain
ComponentsAnaphase-promoting complex subunit 11
KeywordsLIGASE / RING domain / E3 Ubiquitin Ligase
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 / ubiquitin-ubiquitin ligase activity / Regulation of APC/C activators between G1/S and early anaphase / cullin family protein binding / 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 / Separation of Sister Chromatids / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein ubiquitination / cell division / nucleolus / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Anaphase-promoting complex subunit 11, RING-H2 finger / Anaphase-promoting complex subunit 11 RING-H2 finger / : / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Anaphase-promoting complex subunit 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.755 Å
AuthorsBrown, N.G. / Watson, E.R. / Weissmann, F. / Jarvis, M.A. / Vanderlinden, R. / Grace, C.R.R. / Frye, J.J. / Dube, P. / Qiao, R. / Petzold, G. ...Brown, N.G. / Watson, E.R. / Weissmann, F. / Jarvis, M.A. / Vanderlinden, R. / Grace, C.R.R. / Frye, J.J. / Dube, P. / Qiao, R. / Petzold, G. / Cho, S.E. / Alsharif, O. / Bao, J. / Zheng, J. / Nourse, A. / Kurinov, I. / Peters, J.M. / Stark, H. / Schulman, B.A.
CitationJournal: Mol Cell / Year: 2014
Title: Mechanism of polyubiquitination by human anaphase-promoting complex: RING repurposing for ubiquitin chain assembly.
Authors: Nicholas G Brown / Edmond R Watson / Florian Weissmann / Marc A Jarvis / Ryan VanderLinden / Christy R R Grace / Jeremiah J Frye / Renping Qiao / Prakash Dube / Georg Petzold / Shein Ei Cho ...Authors: Nicholas G Brown / Edmond R Watson / Florian Weissmann / Marc A Jarvis / Ryan VanderLinden / Christy R R Grace / Jeremiah J Frye / Renping Qiao / Prakash Dube / Georg Petzold / Shein Ei Cho / Omar Alsharif / Ju Bao / Iain F Davidson / Jie J Zheng / Amanda Nourse / Igor Kurinov / Jan-Michael Peters / Holger Stark / Brenda A Schulman /
Abstract: Polyubiquitination by E2 and E3 enzymes is a predominant mechanism regulating protein function. Some RING E3s, including anaphase-promoting complex/cyclosome (APC), catalyze polyubiquitination by ...Polyubiquitination by E2 and E3 enzymes is a predominant mechanism regulating protein function. Some RING E3s, including anaphase-promoting complex/cyclosome (APC), catalyze polyubiquitination by sequential reactions with two different E2s. An initiating E2 ligates ubiquitin to an E3-bound substrate. Another E2 grows a polyubiquitin chain on the ubiquitin-primed substrate through poorly defined mechanisms. Here we show that human APC's RING domain is repurposed for dual functions in polyubiquitination. The canonical RING surface activates an initiating E2-ubiquitin intermediate for substrate modification. However, APC engages and activates its specialized ubiquitin chain-elongating E2 UBE2S in ways that differ from current paradigms. During chain assembly, a distinct APC11 RING surface helps deliver a substrate-linked ubiquitin to accept another ubiquitin from UBE2S. Our data define mechanisms of APC/UBE2S-mediated polyubiquitination, reveal diverse functions of RING E3s and E2s, and provide a framework for understanding distinctive RING E3 features specifying ubiquitin chain elongation.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anaphase-promoting complex subunit 11
B: Anaphase-promoting complex subunit 11
C: Anaphase-promoting complex subunit 11
D: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,41016
Polymers31,6254
Non-polymers78512
Water3,747208
1
A: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1024
Polymers7,9061
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1024
Polymers7,9061
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1024
Polymers7,9061
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1024
Polymers7,9061
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Anaphase-promoting complex subunit 11
B: Anaphase-promoting complex subunit 11
hetero molecules

A: Anaphase-promoting complex subunit 11
B: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,41016
Polymers31,6254
Non-polymers78512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area9830 Å2
ΔGint-77 kcal/mol
Surface area12530 Å2
MethodPISA
6
C: Anaphase-promoting complex subunit 11
D: Anaphase-promoting complex subunit 11
hetero molecules

C: Anaphase-promoting complex subunit 11
D: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,41016
Polymers31,6254
Non-polymers78512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area9860 Å2
ΔGint-77 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.446, 39.876, 65.038
Angle α, β, γ (deg.)90.00, 108.49, 90.00
Int Tables number3
Space group name H-MP121
DetailsThe structure is of a domain-swapped dimer. The domain swap occurs at VAL 69. To generate the biological unit, it is necessary to pair residues 21-68 from Chain A with 69-84 of Chain B, residues 21-68 from Chain B with 69-84 of Chain A, residues 20-68 of Chain C with 69-84 of Chain D, and 20-68 of Chain D with 69-84 of Chain C.

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Components

#1: Protein
Anaphase-promoting complex subunit 11 / APC11 / Cyclosome subunit 11 / Hepatocellular carcinoma-associated RING finger protein


Mass: 7906.229 Da / Num. of mol.: 4 / Fragment: RING domain (UNP Residues 17-84)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC11, HSPC214 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NYG5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG3350, 0.2 M NaNO3, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2827 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2014
RadiationMonochromator: CRYO-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 1.755→61.681 Å / Num. obs: 24444 / % possible obs: 94.59 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.755→1.85 Å / % possible all: 80.2

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Processing

Software
NameVersionClassification
XDS-RAPDdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDS-RAPDdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.755→61.681 Å / SU ML: 0.46 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 2000 8.18 %Random
Rwork0.1923 ---
all0.1954 ---
obs0.1954 24442 94.59 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.012 Å2 / ksol: 0.401 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4649 Å20 Å2-0.2186 Å2
2---0.0458 Å2-0 Å2
3---0.5107 Å2
Refinement stepCycle: LAST / Resolution: 1.755→61.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 12 208 2228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082098
X-RAY DIFFRACTIONf_angle_d1.1692829
X-RAY DIFFRACTIONf_dihedral_angle_d18.125765
X-RAY DIFFRACTIONf_chiral_restr0.083271
X-RAY DIFFRACTIONf_plane_restr0.007368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.755-1.79890.33771040.3181166X-RAY DIFFRACTION69
1.7989-1.84750.2671310.25991475X-RAY DIFFRACTION88
1.8475-1.90190.28411450.21931612X-RAY DIFFRACTION96
1.9019-1.96330.27651420.20421610X-RAY DIFFRACTION96
1.9633-2.03350.2331470.18591637X-RAY DIFFRACTION97
2.0335-2.11490.23281440.18581618X-RAY DIFFRACTION96
2.1149-2.21110.20321450.18631639X-RAY DIFFRACTION97
2.2111-2.32770.25281480.18371645X-RAY DIFFRACTION97
2.3277-2.47360.21461430.18711614X-RAY DIFFRACTION96
2.4736-2.66460.24111490.18931670X-RAY DIFFRACTION98
2.6646-2.93270.23081480.19611666X-RAY DIFFRACTION98
2.9327-3.3570.23961490.18391661X-RAY DIFFRACTION98
3.357-4.22940.19381500.16711695X-RAY DIFFRACTION99
4.2294-61.71950.20921550.19991734X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 43.5023 Å / Origin y: 1.6788 Å / Origin z: 15.4601 Å
111213212223313233
T0.0852 Å20.0071 Å2-0.0082 Å2-0.0658 Å2-0.0101 Å2--0.0985 Å2
L0.3214 °20.1101 °2-0.2524 °2-0.2878 °20.0426 °2--0.704 °2
S0.0253 Å °0.045 Å °0.0181 Å °0.0137 Å °0.046 Å °-0.0665 Å °0.0032 Å °-0.0127 Å °-0.0689 Å °
Refinement TLS groupSelection details: all

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