[English] 日本語
Yorodumi
- PDB-3cmm: Crystal Structure of the Uba1-Ubiquitin Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cmm
TitleCrystal Structure of the Uba1-Ubiquitin Complex
Components
  • Ubiquitin
  • Ubiquitin-activating enzyme E1 1
KeywordsLIGASE/PROTEIN BINDING / Ubiquitin / E1 / Uba1 / Protein turnover / ligase / Conformational change / thioester / adenylation / transthioesterification / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Ubl conjugation pathway / DNA damage / DNA repair / LIGASE-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


: / : / : / : / : / Regulation of TP53 Degradation / : / RAS processing / Regulation of PTEN localization / : ...: / : / : / : / : / Regulation of TP53 Degradation / : / RAS processing / Regulation of PTEN localization / : / UCH proteinases / : / Aggrephagy / Pexophagy / PINK1-PRKN Mediated Mitophagy / : / Peroxisomal protein import / : / ABC-family proteins mediated transport / E1 ubiquitin-activating enzyme / : / Endosomal Sorting Complex Required For Transport (ESCRT) / ubiquitin activating enzyme activity / : / Translesion synthesis by REV1 / : / : / : / : / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / : / Formation of the ternary complex, and subsequently, the 43S complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / Ribosomal scanning and start codon recognition / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / Major pathway of rRNA processing in the nucleolus and cytosol / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / Gap-filling DNA repair synthesis and ligation in TC-NER / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / ribosomal large subunit export from nucleus / Ub-specific processing proteases / modification-dependent protein catabolic process / protein tag activity / peroxisome / ribosome biogenesis / ribosomal large subunit assembly / cytosolic large ribosomal subunit / ubiquitin-dependent protein catabolic process / cytoplasmic translation / structural constituent of ribosome / protein ubiquitination / DNA damage response / ubiquitin protein ligase binding / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain ...Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Elongation Factor Tu (Ef-tu); domain 3 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / FAD/NAD(P)-binding domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 3-Layer(bba) Sandwich / : / Ubiquitin-like (UB roll) / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Ubiquitin-like domain superfamily / Roll / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROLINE / Polyubiquitin / Ubiquitin-activating enzyme E1 1 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLee, I. / Schindelin, H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural insights into E1-catalyzed ubiquitin activation and transfer to conjugating enzymes.
Authors: Lee, I. / Schindelin, H.
History
DepositionMar 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-activating enzyme E1 1
C: Ubiquitin-activating enzyme E1 1
B: Ubiquitin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,4006
Polymers244,1694
Non-polymers2302
Water3,171176
1
A: Ubiquitin-activating enzyme E1 1
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2003
Polymers122,0852
Non-polymers1151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-9.6 kcal/mol
Surface area47550 Å2
MethodPISA
2
C: Ubiquitin-activating enzyme E1 1
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2003
Polymers122,0852
Non-polymers1151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-11.7 kcal/mol
Surface area47040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.363, 118.564, 207.567
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
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPHEPHEAA14 - 9055 - 896
21ILEILEPHEPHECB14 - 9055 - 896
12METMETGLYGLYBC1 - 761 - 76
22METMETGLYGLYDD1 - 761 - 76

NCS ensembles :
ID
1
2

-
Components

#1: Protein Ubiquitin-activating enzyme E1 1


Mass: 113515.977 Da / Num. of mol.: 2 / Fragment: Residues 10-1024
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBA1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: P22515, ubiquitin-protein ligase
#2: Protein Ubiquitin


Mass: 8568.769 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBI1, RPL40A / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61864, UniProt: P0CG63*PLUS
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: L-proline, PEG 5000 MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 77706 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 7.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.412 / % possible all: 86.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
PHASERphasing
RefinementResolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.901 / SU B: 25.795 / SU ML: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.029 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24687 3899 5 %RANDOM
Rwork0.19077 ---
obs0.19365 73486 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17051 0 14 176 17241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02217403
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9723536
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28952152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15525.394825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.808153100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1191574
X-RAY DIFFRACTIONr_chiral_restr0.0990.22639
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213144
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.27770
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.211833
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2601
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4131.510973
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.737217451
X-RAY DIFFRACTIONr_scbond_it1.22837042
X-RAY DIFFRACTIONr_scangle_it2.0844.56085
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3512medium positional0.50.5
2B304medium positional0.20.5
1A3408loose positional0.75
2B297loose positional0.475
1A3512medium thermal0.442
2B304medium thermal0.382
1A3408loose thermal1.0510
2B297loose thermal0.9610
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 229 -
Rwork0.286 4539 -
obs--84.12 %
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)
12.81820.2077-0.09251.1996-0.36311.44850.0873-0.370.09690.1637-0.05120.0182-0.22020.0187-0.0361-0.0982-0.0396-0.004-0.1361-0.0535-0.175511.212.334-29.882
24.83310.67721.12855.50231.05196.32090.09950.3379-0.63770.00120.04720.08810.40920.0124-0.1467-0.0957-0.0016-0.0411-0.1525-0.0778-0.0542-20.768-7.428-52.814
32.66150.5036-0.46731.8641-0.35411.6196-0.0040.49910.1271-0.24530.03180.1219-0.18670.1081-0.0277-0.0848-0.0329-0.0254-0.08060.0075-0.138117.97316.172-54.321
42.66260.65840.15936.3927-1.00012.05-0.07820.44990.0695-0.6860.1025-0.4454-0.01930.1545-0.0243-0.0853-0.02120.02940.0768-0.0255-0.1763-18.46619.337-76.451
52.72852.3229-0.51063.64170.35078.4079-0.19140.7176-0.1348-0.68690.5592-0.5954-0.23750.7536-0.36780.0486-0.05580.06510.526-0.21280.006231.7084.89-83.232
69.26330.04280.979510.64171.21292.13610.23590.7776-1.5325-0.29240.03960.10410.3420.052-0.2756-0.0291-0.017-0.0325-0.0388-0.19280.25227.234-10.833-53.038
72.5352-0.2628-0.29251.1354-0.12091.28750.07120.30840.1156-0.1311-0.0525-0.0331-0.13940.0473-0.0187-0.0506-0.03020.0073-0.13510.0119-0.194-43.50324.102-44.442
83.7969-0.17440.82865.4484-0.77856.45010.0981-0.1795-0.5480.0120.1224-0.04170.6147-0.0362-0.2205-0.0276-0.0151-0.0086-0.16540.0115-0.012-21.182-11.038-29.448
91.8456-0.1228-0.56951.86410.06531.47960.0137-0.34010.02150.3935-0.0049-0.0066-0.1567-0.0263-0.0087-0.0222-0.03770.0065-0.0783-0.0163-0.1848-50.45821.701-19.911
102.3395-0.3794-3.25742.0797-2.4098.81030.221-0.36390.27220.38330.22540.0271-0.308-0.2373-0.44640.0758-0.05180.08060.30450.06640.0511-71.4666.4133.334
112.4266-0.5651-0.15062.51740.8613.257-0.0906-0.3527-0.13960.48780.16330.01630.09830.0613-0.07270.01270.0001-0.02560.00440.0527-0.1913-15.7177.2710.956
124.8457-0.31260.59416.3775-0.12372.443-0.0056-0.0303-0.9605-0.1580.06680.15110.4265-0.065-0.06110.0026-0.06710.0146-0.082-0.00160.0675-48.594-5.399-29.829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 1773 - 168
2X-RAY DIFFRACTION1AA263 - 426254 - 417
3X-RAY DIFFRACTION2AA178 - 262169 - 253
4X-RAY DIFFRACTION3AA427 - 596418 - 587
5X-RAY DIFFRACTION3AA862 - 916853 - 907
6X-RAY DIFFRACTION4AA597 - 860588 - 851
7X-RAY DIFFRACTION5AA920 - 1024911 - 1015
8X-RAY DIFFRACTION6BC1 - 761 - 76
9X-RAY DIFFRACTION7CB12 - 1773 - 168
10X-RAY DIFFRACTION7CB263 - 426254 - 417
11X-RAY DIFFRACTION8CB178 - 262169 - 253
12X-RAY DIFFRACTION9CB427 - 596418 - 587
13X-RAY DIFFRACTION9CB862 - 916853 - 907
14X-RAY DIFFRACTION10CB920 - 1024911 - 1015
15X-RAY DIFFRACTION11CB597 - 860588 - 851
16X-RAY DIFFRACTION12DD1 - 761 - 76

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more