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- PDB-6njg: Ubiquitin Variant in Complex with Ubiquitin Interacting Motif -

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Basic information

Entry
Database: PDB / ID: 6njg
TitleUbiquitin Variant in Complex with Ubiquitin Interacting Motif
Components
  • Polyubiquitin-B
  • Vacuolar protein sorting-associated protein 27Vacuole
KeywordsPROTEIN BINDING / Ubiquitin Variant / UIM
Function / homology
Function and homology information


microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / microautophagy / ATP export / protein retention in Golgi apparatus / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / multivesicular body sorting pathway / late endosome to vacuole transport ...microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / microautophagy / ATP export / protein retention in Golgi apparatus / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / multivesicular body sorting pathway / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / vacuolar membrane / protein secretion / ubiquitin binding / endosome membrane / endosome / protein heterodimerization activity / protein domain specific binding / protein-containing complex / metal ion binding / nucleus
Similarity search - Function
: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM ...: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Ubiquitin interaction motif / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Zinc finger, FYVE/PHD-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin B / Vacuolar protein sorting-associated protein 27
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsManczyk, N. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-143277 Canada
CitationJournal: Protein Sci. / Year: 2019
Title: Dimerization of a ubiquitin variant leads to high affinity interactions with a ubiquitin interacting motif.
Authors: Manczyk, N. / Veggiani, G. / Gish, G.D. / Yates, B.P. / Ernst, A. / Sidhu, S.S. / Sicheri, F.
History
DepositionJan 3, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionMar 6, 2019ID: 5UCL
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Vacuolar protein sorting-associated protein 27
C: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)12,5662
Polymers12,5662
Non-polymers00
Water1448
1
B: Vacuolar protein sorting-associated protein 27
C: Polyubiquitin-B

B: Vacuolar protein sorting-associated protein 27
C: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)25,1324
Polymers25,1324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_667-y+1,-x+1,-z+5/21
Buried area7620 Å2
ΔGint-55 kcal/mol
Surface area8750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.613, 44.613, 104.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein/peptide Vacuolar protein sorting-associated protein 27 / Vacuole / Golgi retention defective protein 11


Mass: 2824.103 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40343
#2: Protein Polyubiquitin-B


Mass: 9742.091 Da / Num. of mol.: 1
Mutation: K6Q, L8I, G10V, K11M, T12R, T14A, K48M, Q62K, K63R, E64D, T66N, H68Y, L71S, R72S, G75S, G76L, M77R, Q78A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.1 M DL-Malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 4788 / % possible obs: 98.3 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 31.5
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3.41 / Num. unique all: 424 / CC1/2: 0.96 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211:000)refinement
REFMAC5.8.0103refinement
HKL-20002000.0.98.706data reduction
HKL-20002000.0.98.706data scaling
PHASER6.5.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q0W, 1UBQ

1q0w

1ubq


Resolution: 2.35→27.43 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 240 5.06 %RANDOM
Rwork0.2065 ---
obs0.2086 4747 98.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms718 0 0 8 726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012725
X-RAY DIFFRACTIONf_angle_d1.251982
X-RAY DIFFRACTIONf_dihedral_angle_d3.62454
X-RAY DIFFRACTIONf_chiral_restr0.065120
X-RAY DIFFRACTIONf_plane_restr0.007127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3458-2.95490.35431150.25952157X-RAY DIFFRACTION98
2.9549-27.43190.22321250.1952350X-RAY DIFFRACTION99
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)
10.3744-1.9829-1.43868.81346.31045.0777-0.0488-0.39210.3206-0.49150.8111-1.1991-0.59972.26070.07150.39960.1329-0.03670.5757-0.05820.485216.018335.9689128.4883
29.3434-3.707-2.28415.51442.14920.9303-0.2761-0.670.76540.7420.315-0.3101-2.2293-0.6016-0.30811.06570.0576-0.05710.4415-0.10040.40075.921140.784149.1089
33.6923-3.57073.85527.8655-3.24537.685-1.3968-0.05421.2781-0.43350.33440.3782-2.3067-1.5917-0.53990.54890.05440.08340.4726-0.06590.60065.485538.1633133.9432
43.183-3.06151.07288.32621.14152.1413-0.83031.74550.07490.1409-0.5816-1.7864-0.1644-1.4795-0.05490.6738-0.0107-0.04750.85830.13080.68130.98239.4382118.7929
57.7922-0.9802-0.79871.44011.43424.54871.74223.51750.7357-0.7386-0.6042-0.1249-0.5791-1.1294-0.01840.89070.36140.35311.01730.27970.75778.476446.1595107.0155
65.3561-2.3439-4.76653.91471.83544.72510.04450.36131.7737-0.3753-0.1670.1129-1.6976-0.68550.03160.6150.113-0.14530.61960.07610.59746.311549.4491117.4113
73.56820.2521-3.26534.3254.18947.7971-0.5714-0.08831.57611.07320.7316-1.2932-1.1659-0.24120.11060.84950.0796-0.10740.5081-0.07560.663211.127147.2568123.7447
85.5973-2.4664-2.06064.4296-2.25714.5063-0.16490.23570.3362-1.0159-0.3566-1.6531-1.14350.4413-0.08060.7771-0.00510.11150.5439-0.03740.561317.514541.9503114.0257
91.553-1.8161.01942.647-2.35693.16880.51960.98870.3217-0.77310.07090.31940.0009-1.462-0.40660.807-0.0463-0.03111.0669-0.04180.671810.625437.1505109.1962
105.2468-4.232-3.69143.60272.49993.32930.09661.14951.22590.051-0.5540.2074-0.4183-1.30570.16470.72730.1436-0.07180.6283-0.05620.64817.445943.492128.3241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 255 through 271 )
2X-RAY DIFFRACTION2chain 'C' and (resid 1 through 5 )
3X-RAY DIFFRACTION3chain 'C' and (resid 6 through 10 )
4X-RAY DIFFRACTION4chain 'C' and (resid 11 through 15 )
5X-RAY DIFFRACTION5chain 'C' and (resid 16 through 22 )
6X-RAY DIFFRACTION6chain 'C' and (resid 23 through 34 )
7X-RAY DIFFRACTION7chain 'C' and (resid 35 through 44 )
8X-RAY DIFFRACTION8chain 'C' and (resid 45 through 56 )
9X-RAY DIFFRACTION9chain 'C' and (resid 57 through 67 )
10X-RAY DIFFRACTION10chain 'C' and (resid 68 through 76 )

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