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- PDB-3kyc: Human SUMO E1 complex with a SUMO1-AMP mimic -

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Basic information

Entry
Database: PDB / ID: 3kyc
TitleHuman SUMO E1 complex with a SUMO1-AMP mimic
Components
  • (SUMO-activating enzyme subunit ...) x 2
  • Small ubiquitin-related modifier 1
KeywordsLIGASE / E1 / SUMO / UBIQUITIN / THIOESTER / ADENYLATION / INHIBITOR / ACYL-ADENYLATE INTERMEDIATE / Acetylation / Nucleus / Phosphoprotein / Ubl conjugation pathway / ATP-binding / Nucleotide-binding / Polymorphism / Cytoplasm / Isopeptide bond / Membrane
Function / homology
Function and homology information


SUMO activating enzyme complex / SUMO activating enzyme activity / ubiquitin activating enzyme activity / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule ...SUMO activating enzyme complex / SUMO activating enzyme activity / ubiquitin activating enzyme activity / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / SUMO binding / small protein activating enzyme binding / positive regulation of protein sumoylation / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of immune response proteins / ATP-dependent protein binding / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / ubiquitin-like protein conjugating enzyme binding / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / positive regulation of protein targeting to mitochondrion / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / SUMOylation of ubiquitinylation proteins / roof of mouth development / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / enzyme activator activity / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / Formation of Incision Complex in GG-NER / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / transferase activity / nuclear membrane / protein stabilization / nuclear body / nuclear speck / protein heterodimerization activity / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / magnesium ion binding / enzyme binding / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. ...SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Small ubiquitin-related modifier 1, Ubl domain / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / NAD(P)-binding Rossmann-like Domain / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-deoxy-5'-(sulfamoylamino)adenosine / Small ubiquitin-related modifier 1 / SUMO-activating enzyme subunit 1 / SUMO-activating enzyme subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsLima, C.D.
CitationJournal: Nature / Year: 2010
Title: Active site remodelling accompanies thioester bond formation in the SUMO E1.
Authors: Olsen, S.K. / Capili, A.D. / Lu, X. / Tan, D.S. / Lima, C.D.
History
DepositionDec 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUMO-activating enzyme subunit 1
B: SUMO-activating enzyme subunit 2
D: Small ubiquitin-related modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5645
Polymers123,1533
Non-polymers4112
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-38 kcal/mol
Surface area40380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.174, 133.365, 159.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a heterotrimer.

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Components

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SUMO-activating enzyme subunit ... , 2 types, 2 molecules AB

#1: Protein SUMO-activating enzyme subunit 1 / Ubiquitin-like 1-activating enzyme E1A


Mass: 38499.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AOS1, SAE1, SUA1, UBLE1A / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 CP RIL / References: UniProt: Q9UBE0
#2: Protein SUMO-activating enzyme subunit 2 / Ubiquitin-like 1-activating enzyme E1B / Anthracycline-associated resistance ARX


Mass: 73501.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRIHFB2115, SAE2, UBA2, UBLE1B / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 CP RIL
References: UniProt: Q9UBT2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Protein , 1 types, 1 molecules D

#3: Protein Small ubiquitin-related modifier 1 / SUMO-1 / Sentrin / Ubiquitin-like protein SMT3C / SMT3 homolog 3 / Ubiquitin-homology domain ...SUMO-1 / Sentrin / Ubiquitin-like protein SMT3C / SMT3 homolog 3 / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein UBL1 / GAP-modifying protein 1 / GMP1


Mass: 11151.584 Da / Num. of mol.: 1 / Fragment: UNP residues 1-97 / Mutation: T95C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 CP RIL / References: UniProt: P63165

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Non-polymers , 3 types, 255 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Details: cysteylglycylglycyl 5'-(sulfamoylaminodeoxy)adenosine
#5: Chemical ChemComp-JZU / 5'-deoxy-5'-(sulfamoylamino)adenosine


Mass: 345.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N7O5S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsLIGAND CYS-GLY-GLY-AMSN, WHERE AMSN HAS ID JZU IN THIS FILE, WAS LINKED TO SUMO1 BY INTEIN-MEDIATED ...LIGAND CYS-GLY-GLY-AMSN, WHERE AMSN HAS ID JZU IN THIS FILE, WAS LINKED TO SUMO1 BY INTEIN-MEDIATED LIGATION TO MAKE CHAIN D.
Sequence detailsCHAIN D IS COMPOSED AS UB/UBI-CYS-GLY-GLY-AMSN, ADENYLATE MIMIC.

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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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1 MES, 24% PEG 3350, 1.3 M AMMONIUM ACETATE, 10 mM ATP, 10 mM MgCl2, 10 mM TCEP, 2.5% PEG 400, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→25 Å / Num. obs: 47106 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.3
Reflection shellResolution: 2.45→2.51 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.2 / % possible all: 98

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0093refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y8Q

1y8q


Resolution: 2.45→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.958 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2378 5.1 %RANDOM
Rwork0.191 ---
obs0.194 46977 99.2 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 149.48 Å2 / Biso mean: 71.486 Å2 / Biso min: 26.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--3.38 Å20 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.45→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7404 0 24 253 7681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0227560
X-RAY DIFFRACTIONr_angle_refined_deg1.951.97610203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2495933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37124.684348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.394151387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2061548
X-RAY DIFFRACTIONr_chiral_restr0.130.21147
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215643
X-RAY DIFFRACTIONr_mcbond_it1.021.54674
X-RAY DIFFRACTIONr_mcangle_it1.9127543
X-RAY DIFFRACTIONr_scbond_it2.77432886
X-RAY DIFFRACTIONr_scangle_it4.54.52660
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 170 -
Rwork0.325 3216 -
all-3386 -
obs--98 %

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