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- PDB-5vmd: Crystal structure of UBR-box from UBR6 in a domain-swapping confo... -

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Basic information

Entry
Database: PDB / ID: 5vmd
TitleCrystal structure of UBR-box from UBR6 in a domain-swapping conformation
ComponentsF-box only protein 11
KeywordsLIGASE / domain swapping / zinc finger / zinc / ubr-box / ubr6 / fbxo11
Function / homology
Function and homology information


protein modification process => GO:0036211 / protein-arginine N-methyltransferase activity / ubiquitin ligase complex / post-translational protein modification / sensory perception of sound / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / chromosome / Neddylation ...protein modification process => GO:0036211 / protein-arginine N-methyltransferase activity / ubiquitin ligase complex / post-translational protein modification / sensory perception of sound / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / chromosome / Neddylation / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein ubiquitination / nucleolus / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
F-box only protein 11 / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat-2 / Putative zinc finger in N-recognin (UBR box) / Periplasmic copper-binding protein NosD, beta helix domain / Periplasmic copper-binding protein (NosD) / Carbohydrate-binding/sugar hydrolysis domain / Domain present in carbohydrate binding proteins and sugar hydrolses / Zinc finger, UBR-type ...F-box only protein 11 / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat-2 / Putative zinc finger in N-recognin (UBR box) / Periplasmic copper-binding protein NosD, beta helix domain / Periplasmic copper-binding protein (NosD) / Carbohydrate-binding/sugar hydrolysis domain / Domain present in carbohydrate binding proteins and sugar hydrolses / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / Parallel beta-helix repeat / Parallel beta-helix repeats / F-box domain / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
F-box only protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.202 Å
AuthorsMunoz-Escobar, J. / Kozlov, G. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Protein Sci. / Year: 2017
Title: Crystal structure of the UBR-box from UBR6/FBXO11 reveals domain swapping mediated by zinc binding.
Authors: Munoz-Escobar, J. / Kozlov, G. / Gehring, K.
History
DepositionApr 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Aug 9, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.ptnr2_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box only protein 11
B: F-box only protein 11
C: F-box only protein 11
D: F-box only protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,96127
Polymers34,4874
Non-polymers1,47423
Water2,108117
1
A: F-box only protein 11
C: F-box only protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,01214
Polymers17,2432
Non-polymers76812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-159 kcal/mol
Surface area10480 Å2
MethodPISA
2
B: F-box only protein 11
D: F-box only protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,95013
Polymers17,2432
Non-polymers70611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-153 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.570, 69.200, 82.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 835:856 or (resid 861 and (name...
21(chain B and (resseq 835:856 or (resid 861 and (name...
31(chain C and (resseq 835:856 or (resid 861 and (name...
41(chain D and (resseq 835:856 or (resid 861 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSCYSCYS(chain A and (resseq 835:856 or (resid 861 and (name...AA835 - 8568 - 29
12ARGARGARGARG(chain A and (resseq 835:856 or (resid 861 and (name...AA86134
13GLNGLNALAALA(chain A and (resseq 835:856 or (resid 861 and (name...AA834 - 9027 - 75
14GLNGLNALAALA(chain A and (resseq 835:856 or (resid 861 and (name...AA834 - 9027 - 75
15GLNGLNALAALA(chain A and (resseq 835:856 or (resid 861 and (name...AA834 - 9027 - 75
16GLNGLNALAALA(chain A and (resseq 835:856 or (resid 861 and (name...AA834 - 9027 - 75
17GLNGLNALAALA(chain A and (resseq 835:856 or (resid 861 and (name...AA834 - 9027 - 75
18GLNGLNALAALA(chain A and (resseq 835:856 or (resid 861 and (name...AA834 - 9027 - 75
19GLNGLNALAALA(chain A and (resseq 835:856 or (resid 861 and (name...AA834 - 9027 - 75
110GLNGLNALAALA(chain A and (resseq 835:856 or (resid 861 and (name...AA834 - 9027 - 75
21CYSCYSCYSCYS(chain B and (resseq 835:856 or (resid 861 and (name...BB835 - 8568 - 29
22ARGARGARGARG(chain B and (resseq 835:856 or (resid 861 and (name...BB86134
23GLYGLYLEULEU(chain B and (resseq 835:856 or (resid 861 and (name...BB-4 - 9011 - 74
24GLYGLYLEULEU(chain B and (resseq 835:856 or (resid 861 and (name...BB-4 - 9011 - 74
25GLYGLYLEULEU(chain B and (resseq 835:856 or (resid 861 and (name...BB-4 - 9011 - 74
26GLYGLYLEULEU(chain B and (resseq 835:856 or (resid 861 and (name...BB-4 - 9011 - 74
27GLYGLYLEULEU(chain B and (resseq 835:856 or (resid 861 and (name...BB-4 - 9011 - 74
28GLYGLYLEULEU(chain B and (resseq 835:856 or (resid 861 and (name...BB-4 - 9011 - 74
29GLYGLYLEULEU(chain B and (resseq 835:856 or (resid 861 and (name...BB-4 - 9011 - 74
210GLYGLYLEULEU(chain B and (resseq 835:856 or (resid 861 and (name...BB-4 - 9011 - 74
31CYSCYSCYSCYS(chain C and (resseq 835:856 or (resid 861 and (name...CC835 - 8568 - 29
32ARGARGARGARG(chain C and (resseq 835:856 or (resid 861 and (name...CC86134
33GLYGLYLEULEU(chain C and (resseq 835:856 or (resid 861 and (name...CC-4 - 9011 - 74
34GLYGLYLEULEU(chain C and (resseq 835:856 or (resid 861 and (name...CC-4 - 9011 - 74
35GLYGLYLEULEU(chain C and (resseq 835:856 or (resid 861 and (name...CC-4 - 9011 - 74
36GLYGLYLEULEU(chain C and (resseq 835:856 or (resid 861 and (name...CC-4 - 9011 - 74
37GLYGLYLEULEU(chain C and (resseq 835:856 or (resid 861 and (name...CC-4 - 9011 - 74
38GLYGLYLEULEU(chain C and (resseq 835:856 or (resid 861 and (name...CC-4 - 9011 - 74
39GLYGLYLEULEU(chain C and (resseq 835:856 or (resid 861 and (name...CC-4 - 9011 - 74
310GLYGLYLEULEU(chain C and (resseq 835:856 or (resid 861 and (name...CC-4 - 9011 - 74
41CYSCYSCYSCYS(chain D and (resseq 835:856 or (resid 861 and (name...DD835 - 8568 - 29
42ARGARGARGARG(chain D and (resseq 835:856 or (resid 861 and (name...DD86134
43GLYGLYLEULEU(chain D and (resseq 835:856 or (resid 861 and (name...DD833 - 9016 - 74
44GLYGLYLEULEU(chain D and (resseq 835:856 or (resid 861 and (name...DD833 - 9016 - 74
45GLYGLYLEULEU(chain D and (resseq 835:856 or (resid 861 and (name...DD833 - 9016 - 74
46GLYGLYLEULEU(chain D and (resseq 835:856 or (resid 861 and (name...DD833 - 9016 - 74
47GLYGLYLEULEU(chain D and (resseq 835:856 or (resid 861 and (name...DD833 - 9016 - 74
48GLYGLYLEULEU(chain D and (resseq 835:856 or (resid 861 and (name...DD833 - 9016 - 74
49GLYGLYLEULEU(chain D and (resseq 835:856 or (resid 861 and (name...DD833 - 9016 - 74
410GLYGLYLEULEU(chain D and (resseq 835:856 or (resid 861 and (name...DD833 - 9016 - 74

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Components

#1: Protein
F-box only protein 11 / Protein arginine N-methyltransferase 9 / Vitiligo-associated protein 1 / VIT-1 / UBR6/FBXO11


Mass: 8621.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO11, FBX11, PRMT9, VIT1, UG063H01 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q86XK2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium nitrate, 0.1 M Bis-Tris propane, pH 6.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.2822 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 2.2→41.72 Å / Num. obs: 20183 / % possible obs: 99.81 % / Redundancy: 4.3 % / CC1/2: 0.851 / Rrim(I) all: 0.094 / Net I/σ(I): 14.67
Reflection shellResolution: 2.202→2.281 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.88 / Num. unique obs: 1952 / Rrim(I) all: 0.608 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.202→41.72 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.88 / Details: Phasing using Zn anomalous signal
RfactorNum. reflection% reflection
Rfree0.2474 1010 5.01 %
Rwork0.1947 --
obs0.1974 20172 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.202→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 50 117 2377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052292
X-RAY DIFFRACTIONf_angle_d0.6843068
X-RAY DIFFRACTIONf_dihedral_angle_d13.2891337
X-RAY DIFFRACTIONf_chiral_restr0.046318
X-RAY DIFFRACTIONf_plane_restr0.004396
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1095X-RAY DIFFRACTION9.592TORSIONAL
12B1095X-RAY DIFFRACTION9.592TORSIONAL
13C1095X-RAY DIFFRACTION9.592TORSIONAL
14D1095X-RAY DIFFRACTION9.592TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2016-2.31770.34991400.2752656X-RAY DIFFRACTION99
2.3177-2.46290.28811420.23022701X-RAY DIFFRACTION100
2.4629-2.6530.28021430.22262709X-RAY DIFFRACTION100
2.653-2.920.31781430.21972707X-RAY DIFFRACTION100
2.92-3.34240.22311440.1972741X-RAY DIFFRACTION100
3.3424-4.21080.20131450.16452761X-RAY DIFFRACTION100
4.2108-48.35680.24321530.18412887X-RAY DIFFRACTION100
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)
15.79641.7143-1.9627.04491.2329.1590.5139-0.74630.31380.8464-0.37170.0648-1.48140.0401-0.16820.7219-0.1010.02370.49160.11840.448926.0266-11.491651.8478
23.15384.14040.1516.92830.84481.5313-0.17750.08870.3916-0.17070.2373-0.1251-0.13150.2861-0.06460.3528-0.00530.05060.5193-0.09080.32752.83251.076449.7834
38.22644.3167.40381.85683.71176.44860.3109-0.52230.01080.0441-0.2217-0.217-0.067-0.2938-0.15530.3096-0.04690.05420.4526-0.00960.305238.4555-0.52942.9063
48.3547-0.9372.36724.00313.50494.3542-0.2020.58930.8560.04590.57140.2107-1.3987-0.9552-0.24110.55570.09460.04910.62450.16050.526729.62124.752130.4719
55.14940.85093.61885.21942.98475.57910.1807-0.28720.24410.1336-0.3499-0.17330.11780.010.20960.29690.06510.05580.4718-0.01590.384340.681426.068886.6995
66.54472.31972.25063.036-1.12675.13530.3193-0.3653-1.4333-0.2954-0.121-0.55970.8826-0.082-0.15860.39030.0205-0.06280.32380.00930.583831.244-2.385477.7995
72.12020.7975-0.96113.4281-1.75953.4302-0.1097-0.112-0.0784-0.540.0399-0.15730.0390.31860.04880.42790.0169-0.00580.3663-0.06050.347944.692210.686371.0536
88.8618-4.8476-3.43043.07291.17543.69890.11410.3723-0.2393-0.5891-0.1589-0.1575-0.06480.3335-0.01680.3369-0.0064-0.01640.5769-0.0040.348949.671-26.516443.5102
97.841-2.57662.20124.3361-3.66829.27330.16570.72890.3764-0.1528-0.1538-0.1246-0.597-0.0080.0020.3161-0.04280.05410.3860.01180.267541.522-0.568331.9568
107.1734-0.3148-0.43957.1222-0.11895.55750.0315-0.123-0.23890.08290.1391-0.6175-0.31941.0863-0.04660.2917-0.03560.01840.4961-0.04320.292458.1248-5.502549.2772
116.7422-7.5477-4.73916.50265.17792.93070.0663-0.93910.4443-0.34650.2625-0.1806-0.16570.4344-0.24210.3546-0.00830.0110.42420.03880.335124.076916.041269.2909
125.9785-1.702-4.0635.06236.41579.3137-0.3111-0.2762-0.34480.2864-0.10140.35820.37510.43940.25850.44510.10910.05650.4182-0.06760.319244.59755.990464.7474
138.10080.5596-2.77481.4443-0.08684.20560.21670.5019-0.3178-0.3275-0.13690.05670.006-0.2745-0.09210.37510.0956-0.07420.3427-0.0780.325232.60995.460367.0182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 834 through 845 )A834 - 845
2X-RAY DIFFRACTION2chain 'A' and (resid 846 through 877 )A846 - 877
3X-RAY DIFFRACTION3chain 'A' and (resid 878 through 892 )A878 - 892
4X-RAY DIFFRACTION4chain 'A' and (resid 893 through 902 )A893 - 902
5X-RAY DIFFRACTION5chain 'B' and (resid -4 through 845 )B-4 - 845
6X-RAY DIFFRACTION6chain 'B' and (resid 846 through 877 )B846 - 877
7X-RAY DIFFRACTION7chain 'B' and (resid 878 through 901 )B878 - 901
8X-RAY DIFFRACTION8chain 'C' and (resid -4 through 846 )C-4 - 846
9X-RAY DIFFRACTION9chain 'C' and (resid 847 through 884 )C847 - 884
10X-RAY DIFFRACTION10chain 'C' and (resid 885 through 901 )C885 - 901
11X-RAY DIFFRACTION11chain 'D' and (resid 833 through 853 )D833 - 853
12X-RAY DIFFRACTION12chain 'D' and (resid 854 through 865 )D854 - 865
13X-RAY DIFFRACTION13chain 'D' and (resid 866 through 901 )D866 - 901

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