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- PDB-2bwe: The crystal structure of the complex between the UBA and UBL doma... -

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Basic information

Entry
Database: PDB / ID: 2bwe
TitleThe crystal structure of the complex between the UBA and UBL domains of Dsk2
Components(DSK2) x 2
KeywordsSIGNALING PROTEIN / UBIQUITIN / UBIQUITIN-LIKE PROTEINS / PROTEIN/PROTEIN INTERACTION
Function / homology
Function and homology information


Cargo recognition for clathrin-mediated endocytosis / spindle pole body duplication / protein localization to vacuole / polyubiquitin modification-dependent protein binding / ERAD pathway / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / nucleus / cytosol
Similarity search - Function
: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Ubiquitin-associated (UBA) domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 ...: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Ubiquitin-associated (UBA) domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin domain-containing protein DSK2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLowe, E.D. / Hasan, N. / Trempe, J.-F. / Fonso, L. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N. / Brown, N.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structures of the Dsk2 Ubl and Uba Domains and Their Complex.
Authors: Lowe, E.D. / Hasan, N. / Trempe, J.-F. / Fonso, L. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N. / Brown, N.R.
History
DepositionJul 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0May 15, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / database_PDB_rev ...atom_site / database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DSK2
B: DSK2
C: DSK2
D: DSK2
E: DSK2
F: DSK2
G: DSK2
H: DSK2
I: DSK2
J: DSK2
K: DSK2
L: DSK2
M: DSK2
N: DSK2
O: DSK2
P: DSK2
Q: DSK2
R: DSK2
S: DSK2
T: DSK2
U: DSK2


Theoretical massNumber of molelcules
Total (without water)126,68921
Polymers126,68921
Non-polymers00
Water1,820101
1
A: DSK2
B: DSK2
C: DSK2
D: DSK2
E: DSK2
F: DSK2
G: DSK2
H: DSK2
I: DSK2
T: DSK2


Theoretical massNumber of molelcules
Total (without water)59,02710
Polymers59,02710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-16.2 kcal/mol
Surface area31750 Å2
MethodPQS
2
N: DSK2
O: DSK2
P: DSK2
Q: DSK2
R: DSK2
U: DSK2


Theoretical massNumber of molelcules
Total (without water)36,6306
Polymers36,6306
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-21.2 kcal/mol
Surface area20230 Å2
MethodPQS
3
J: DSK2
K: DSK2
L: DSK2
M: DSK2
S: DSK2


Theoretical massNumber of molelcules
Total (without water)31,0315
Polymers31,0315
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-6.6 kcal/mol
Surface area17230 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.361, 88.854, 141.497
Angle α, β, γ (deg.)90.00, 106.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T
211U
12S
22T
32U

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A326 - 370
2111B326 - 370
3111C326 - 370
4111D326 - 370
5111E326 - 370
6111F326 - 370
7111G326 - 370
8111H326 - 370
9111I326 - 370
10111J326 - 370
11111K326 - 370
12111L326 - 370
13111M326 - 370
14111N326 - 370
15111O326 - 370
16111P326 - 370
17111Q326 - 370
18111R326 - 370
1121S3 - 74
2121T3 - 74
3121U3 - 74

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.74662, 0.65886, -0.09194), (-0.66414, 0.74619, -0.04593), (0.03835, 0.09536, 0.9947)15.22963, 15.85378, -16.36996
2given(0.15777, 0.9681, -0.19464), (-0.98683, 0.14747, -0.06643), (-0.0356, 0.20256, 0.97862)38.02905, 23.55966, -29.27322
3given(-0.48521, 0.82686, -0.28439), (-0.86096, -0.50857, -0.00976), (-0.1527, 0.24011, 0.95866)61.50296, 15.84473, -40.81126
4given(-0.79139, 0.34928, -0.5017), (-0.35954, -0.92969, -0.0801), (-0.4944, 0.11699, 0.86133)93.90946, 14.95492, -39.47005
5given(-0.83737, -0.29466, -0.46042), (0.32322, -0.94616, 0.01769), (-0.44084, -0.134, 0.88753)97.65797, -5.90727, -57.20253
6given(-0.44042, -0.81365, -0.37947), (0.85613, -0.50789, 0.09537), (-0.27033, -0.28287, 0.92028)88.9305, -23.17625, -77.81499
7given(0.1928, -0.93519, -0.29708), (0.98103, 0.1775, 0.07791), (-0.02012, -0.30646, 0.95167)75.42363, -24.16298, -100.36301
8given(0.7547, -0.61648, -0.22446), (0.6361, 0.77134, 0.02027), (0.16064, -0.15808, 0.97427)63.15993, -12.69641, -120.93924
9given(-0.74486, -0.66008, 0.09738), (0.66588, -0.74466, 0.04572), (0.04234, 0.0989, 0.9942)-15.87128, -22.22866, -16.36768
10given(-0.1583, -0.96758, 0.19682), (0.9868, -0.14816, 0.0653), (-0.03402, 0.20456, 0.97826)-38.27025, -29.86706, -29.2418
11given(0.48862, -0.82129, 0.29451), (0.85876, 0.51237, 0.00405), (-0.15423, 0.25094, 0.95564)-62.50208, -21.58858, -40.30556
12given(0.78787, -0.35199, 0.50534), (0.36505, 0.92779, 0.0771), (-0.49599, 0.12373, 0.85947)-94.23322, -21.22643, -39.15549
13given(-0.83472, -0.30625, -0.45767), (-0.3354, 0.94189, -0.01855), (0.43676, 0.13802, -0.88893)18.86055, -44.63328, 57.49371
14given(-0.44036, -0.81144, -0.38426), (-0.85415, 0.51049, -0.09914), (0.27661, 0.28456, -0.91789)11.03672, -27.26027, 77.49428
15given(0.18628, -0.93639, -0.29744), (-0.98234, -0.17216, -0.07326), (0.01739, 0.30584, -0.95192)-2.7884, -27.02833, 100.45814
16given(0.76698, -0.60151, -0.22343), (-0.62034, -0.78411, -0.01852), (-0.16405, 0.15281, -0.97454)-15.37999, -38.80547, 120.95715
17given(0.99999, 0.00473, 0.00011), (0.00473, -0.99998, -0.00304), (0.0001, 0.00304, -1)-39.10907, -50.61503, 136.01256
18given(-1, -0.00132, -0.00014), (0.00132, -1, 0.00084), (-0.00014, 0.00084, 1)-0.04513, -6.47015, 0.01532
19given(0.7962, 0.36572, -0.48199), (0.35176, -0.92797, -0.12305), (-0.49227, -0.07157, -0.86749)22.89502, -42.31796, 53.78956

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Components

#1: Protein/peptide
DSK2


Mass: 5599.130 Da / Num. of mol.: 18 / Fragment: UBA DOMAIN, RESIDUES 324-327
Source method: isolated from a genetically manipulated source
Details: UBA DOMAIN OF DSK2, RESIDUES 326-373 OF THE INTACT PROTEIN
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: P48510
#2: Protein DSK2


Mass: 8634.741 Da / Num. of mol.: 3 / Fragment: UBL DOMAIN, RESIDUES 1-75
Source method: isolated from a genetically manipulated source
Details: UBL DOMAIN OF DSK2, RESIDUES 1-75 OF THE INTACT PROTEIN
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: P48510
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAINS A-R CONTAIN THE UBA DOMAIN OF DSK2 CONSISTING OF RESIDUES 328-373 OF THE INTACT PROTEIN ...CHAINS A-R CONTAIN THE UBA DOMAIN OF DSK2 CONSISTING OF RESIDUES 328-373 OF THE INTACT PROTEIN CHAINS S-U CONTAIN THE UBL DOMAIN OF DSK2 CONSISTING OF RESIDUES 1-77 OF THE INTACT PROTEIN

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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: 4.2 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 10-15% METHOXY PEG 5K BUFFERED WITH 0.1M MES PH 6.5 AT 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.1→59.2 Å / Num. obs: 33693 / % possible obs: 99.1 % / Observed criterion σ(I): 6 / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A,B,C,D TETRAMER FROM PDB ENTRY 2BWB

2bwb


Resolution: 3.1→136.08 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.893 / SU B: 42.815 / SU ML: 0.372 / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1707 5.1 %RANDOM
Rwork0.239 ---
obs0.241 31934 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.51 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å21.12 Å2
2---0.32 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 3.1→136.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8309 0 0 101 8410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0218430
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.95211318
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.03951026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.1124.175515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.146151433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5761593
X-RAY DIFFRACTIONr_chiral_restr0.1120.21169
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026714
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.23697
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.25567
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2331
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3421.55196
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6328106
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.08133454
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8794.53212
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A339tight positional0.080.05
12B339tight positional0.060.05
13C339tight positional0.070.05
14D339tight positional0.080.05
15E339tight positional0.070.05
16F339tight positional0.040.05
17G339tight positional0.060.05
18H339tight positional0.040.05
19I339tight positional0.050.05
110J339tight positional0.070.05
111K339tight positional0.070.05
112L339tight positional0.070.05
113M339tight positional0.070.05
114N339tight positional0.050.05
115O339tight positional0.050.05
116P339tight positional0.040.05
117Q339tight positional0.060.05
118R339tight positional0.080.05
21S567tight positional0.030.05
22T567tight positional0.030.05
23U567tight positional0.040.05
11A339tight thermal0.10.5
12B339tight thermal0.110.5
13C339tight thermal0.130.5
14D339tight thermal0.120.5
15E339tight thermal0.090.5
16F339tight thermal0.070.5
17G339tight thermal0.10.5
18H339tight thermal0.070.5
19I339tight thermal0.070.5
110J339tight thermal0.10.5
111K339tight thermal0.130.5
112L339tight thermal0.110.5
113M339tight thermal0.110.5
114N339tight thermal0.080.5
115O339tight thermal0.080.5
116P339tight thermal0.080.5
117Q339tight thermal0.080.5
118R339tight thermal0.110.5
21S567tight thermal0.050.5
22T567tight thermal0.060.5
23U567tight thermal0.070.5
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 117
Rwork0.306 2343

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