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- PDB-3kci: The third RLD domain of HERC2 -

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Basic information

Entry
Database: PDB / ID: 3kci
TitleThe third RLD domain of HERC2
ComponentsProbable E3 ubiquitin-protein ligase HERC2
KeywordsLIGASE / WD40 / RCC1 / STRUCTURAL GENOMICS CONSORTIUM / SGC / Coiled coil / Metal-binding / Phosphoprotein / Ubl conjugation pathway / WD repeat / Zinc / Zinc-finger
Function / homology
Function and homology information


SUMO binding / HECT-type E3 ubiquitin transferase / SUMOylation of DNA damage response and repair proteins / centriole / guanyl-nucleotide exchange factor activity / Nonhomologous End-Joining (NHEJ) / intracellular protein transport / G2/M DNA damage checkpoint / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation ...SUMO binding / HECT-type E3 ubiquitin transferase / SUMOylation of DNA damage response and repair proteins / centriole / guanyl-nucleotide exchange factor activity / Nonhomologous End-Joining (NHEJ) / intracellular protein transport / G2/M DNA damage checkpoint / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / DNA damage response / zinc ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Beta-propeller repeat TECPR / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / CPH domain ...HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Beta-propeller repeat TECPR / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Galactose-binding-like domain superfamily / Ribosomal protein L2, domain 2 / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HERC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWalker, J.R. / Qiu, L. / Vesterberg, A. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
CitationJournal: To be Published
Title: Structure of the Third RLD Domain of Herc2
Authors: Walker, J.R. / Qiu, L. / Vesterberg, A. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionOct 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable E3 ubiquitin-protein ligase HERC2


Theoretical massNumber of molelcules
Total (without water)41,1161
Polymers41,1161
Non-polymers00
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.673, 52.673, 215.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Probable E3 ubiquitin-protein ligase HERC2 / HECT domain and RCC1-like domain-containing protein 2


Mass: 41115.961 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 3951-4321, RCC1-LIKE DOMAIN
Source method: isolated from a genetically manipulated source
Details: HERC2 SYNONYM: JDF2, KIAA0393, P528, SHEP1 / Source: (gene. exp.) Homo sapiens (human) / Gene: D15F37S1, DKFZP547P028, HERC2 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)
References: UniProt: O95714, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 290.9 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG3350, 0.2mM MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.9K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 9, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 30769 / Num. obs: 30769 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.043 / Net I/σ(I): 41.14
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 8.38 / Num. unique all: 2763 / Rsym value: 0.127 / % possible all: 88.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A12

1a12


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.722 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19499 1548 5 %RANDOM
Rwork0.15163 ---
all0.15377 ---
obs0.15377 29137 98.56 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 24.695 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.3 Å20 Å2
2--0.59 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 0 368 3139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212832
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9463847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4345385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13323.684114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45815459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.231519
X-RAY DIFFRACTIONr_chiral_restr0.1150.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212182
X-RAY DIFFRACTIONr_mcbond_it0.6851.51840
X-RAY DIFFRACTIONr_mcangle_it1.15722929
X-RAY DIFFRACTIONr_scbond_it2.0763992
X-RAY DIFFRACTIONr_scangle_it3.2344.5918
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 98 -
Rwork0.157 1882 -
obs--86.43 %
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)
11.67260.35390.17513.03330.75454.6606-0.0839-0.0021-0.39140.0211-0.08110.24490.3247-0.45020.1650.0456-0.07930.040.1573-0.01630.16827.27826.393621.1538
21.7718-2.3492-0.04396.5691-2.19867.6255-0.13760.2543-0.40870.3964-0.09870.75740.327-1.15860.23620.0275-0.12110.05230.3542-0.0480.23261.391128.051522.1332
322.2295-1.15244.53211.57352.30359.6876-0.4673-0.587-0.95830.47150.17650.27320.5996-0.0890.29080.2086-0.04190.15690.1040.07790.208412.332620.355131.2509
41.8935-0.2923-0.29511.67570.08262.4488-0.1542-0.0555-0.27150.16540.01680.14270.1959-0.06520.13740.1147-0.0330.05070.10120.03080.144219.245623.520822.6158
53.2729-1.4076-0.1231.44040.02023.7862-0.16070.0633-0.4730.1294-0.05350.18410.3795-0.19470.21420.1512-0.06950.07310.0284-0.02210.185616.848616.184516.3505
63.58480.1444-0.43517.8451-0.95883.6929-0.1375-0.1729-0.3509-0.0580.11290.08380.38240.07080.02460.14980.05410.0480.09090.06020.110528.591817.690925.734
73.8092-0.1042-0.39017.10961.82161.9063-0.006-0.16220.1282-0.1809-0.14980.41-0.1447-0.20560.15580.0711-0.00520.00750.1299-0.00750.16421.767929.030613.5093
81.2730.3361-0.53111.36010.30972.4101-0.0669-0.0362-0.30460.0578-0.0432-0.01720.3850.11250.110.10510.04120.01050.07940.02040.145931.894620.129713.2548
916.882-12.01-7.468216.95229.655913.17110.03640.04970.04290.3362-0.02-0.5250.41070.3162-0.01630.09110.0494-0.03970.14130.06010.075140.988923.748622.8911
101.58940.2104-0.94241.8145-0.4370.6176-0.0015-0.1415-0.16740.1677-0.0221-0.12560.01430.24830.02350.07550.0217-0.03070.166-0.00310.10935.166331.651217.9058
111.4525-0.4144-0.55862.11870.31972.65760.088-0.0622-0.0155-0.0928-0.0076-0.1870.00180.3482-0.08030.04370.01310.01190.1601-0.00220.112638.360135.06878.9449
121.1542-0.04610.34190.74490.22182.99530.087-0.0497-0.00540.00890.012-0.06680.00130.2723-0.0990.0772-0.0087-0.00410.1658-0.00290.119232.713841.394217.952
131.3075-1.4591-0.78782.08271.17252.69770.26480.2080.2013-0.3356-0.2019-0.109-0.30420.01-0.06290.1340.00490.02090.12530.02830.095728.139248.61027.5242
141.2154-0.4866-0.37520.76650.31931.4330.0756-0.09410.09690.0039-0.0059-0.088-0.1920.0497-0.06980.0862-0.03070.00490.1367-0.00430.096327.229346.574921.137
153.1452-1.0120.17621.5723-0.42182.75480.12580.30830.1063-0.20450.01630.276-0.2731-0.3715-0.14210.10450.0519-0.01460.16280.0130.115812.987648.68912.742
161.24470.0897-0.52621.7273-0.88893.0660.1521-0.06680.21850.0613-0.05930.055-0.6217-0.1618-0.09280.13920.01460.02060.1182-0.00070.126218.835453.207320.1912
171.41380.25180.06671.08830.94473.0140.0434-0.1526-0.02710.0469-0.052-0.0315-0.0749-0.21190.00860.0617-0.01170.00210.16920.01510.113915.504741.031827.7833
182.23170.52760.08131.3878-0.39812.3361-0.03830.1029-0.0178-0.047-0.04390.1641-0.0381-0.38720.08220.02170.0061-0.01440.204-0.00750.09785.459140.059419.6068
193.26761.8988-3.89397.0937-8.34915.02620.0918-0.08870.25280.15580.2230.6281-0.4756-0.4889-0.31480.08810.0313-0.00730.2532-0.00830.18975.794145.423525.5608
202.06740.415-1.73090.79960.2333.16820.0671-0.2158-0.16150.2058-0.0317-0.04390.1981-0.0965-0.03540.0808-0.0277-0.00140.15490.02140.117612.026233.064230.3866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3953 - 3967
2X-RAY DIFFRACTION2A3968 - 3978
3X-RAY DIFFRACTION3A3979 - 3987
4X-RAY DIFFRACTION4A3988 - 4005
5X-RAY DIFFRACTION5A4006 - 4033
6X-RAY DIFFRACTION6A4034 - 4042
7X-RAY DIFFRACTION7A4043 - 4050
8X-RAY DIFFRACTION8A4051 - 4088
9X-RAY DIFFRACTION9A4089 - 4094
10X-RAY DIFFRACTION10A4095 - 4113
11X-RAY DIFFRACTION11A4114 - 4143
12X-RAY DIFFRACTION12A4144 - 4171
13X-RAY DIFFRACTION13A4172 - 4186
14X-RAY DIFFRACTION14A4187 - 4221
15X-RAY DIFFRACTION15A4222 - 4235
16X-RAY DIFFRACTION16A4236 - 4248
17X-RAY DIFFRACTION17A4249 - 4269
18X-RAY DIFFRACTION18A4270 - 4289
19X-RAY DIFFRACTION19A4290 - 4297
20X-RAY DIFFRACTION20A4298 - 4318

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