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- PDB-3kyd: Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic -

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Basic information

Entry
Database: PDB / ID: 3kyd
TitleHuman SUMO E1~SUMO1-AMP tetrahedral intermediate mimic
Components
  • (SUMO-activating enzyme subunit ...) x 2
  • Small ubiquitin-related modifier 1
KeywordsLIGASE / E1 / SUMO / UBIQUITIN / THIOESTER / ADENYLATION / INHIBITOR / TETRAHEDRAL INTERMEDIATE / Nucleus / Phosphoprotein / Ubl conjugation pathway / ATP-binding / Nucleotide-binding / Isopeptide bond / Membrane
Function / homology
Function and homology information


SUMO activating enzyme complex / SUMO activating enzyme activity / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / ubiquitin activating enzyme activity / 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) ...SUMO activating enzyme complex / SUMO activating enzyme activity / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / ubiquitin activating enzyme activity / 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) / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / negative regulation of action potential / positive regulation of protein sumoylation / small protein activating enzyme binding / SUMO binding / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / ATP-dependent protein binding / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / 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 / transcription factor binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / nuclear pore / Regulation of IFNG signaling / SUMOylation of DNA damage response and repair proteins / enzyme activator activity / 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 / negative regulation of DNA-binding transcription factor activity / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / transferase activity / nuclear membrane / nuclear body / protein stabilization / nuclear speck / protein heterodimerization activity / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / magnesium ion 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. / Small ubiquitin-related modifier 1, Ubl domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin-activating enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Ubiquitin-like domain superfamily / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-VMX / 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: 2.61 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: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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)113,9108
Polymers113,2713
Non-polymers6395
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-15 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.717, 115.608, 90.837
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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: 61562.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His6-SMT3 fusion protein (Mossessova and Lima, 2000)
Source: (gene. exp.) Homo sapiens (human) / Gene: HRIHFB2115, SAE2, UBA2, UBLE1B / Plasmid: pSMT3 / 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: 13208.845 Da / Num. of mol.: 1 / Fragment: UNP residues 1-96 / 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: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 CP RIL / References: UniProt: P63165

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Non-polymers , 4 types, 220 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
Details: cysteylglycylglycyl 5'-(vinylsulfonylaminodeoxy)adenosine
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-VMX / 5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine


Mass: 387.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N7O5S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE CYS-GLY-GLY-AVSN LIGAND, WHERE AVSN HAS ID VMX IN THIS FILE, WAS LINKED TO SUMO1 BY INTEIN- ...THE CYS-GLY-GLY-AVSN LIGAND, WHERE AVSN HAS ID VMX IN THIS FILE, WAS LINKED TO SUMO1 BY INTEIN-MEDIATED LIGATION. THERE IS A CROSS-LINK BETWEEN ATOM SG IN RESIDUE CYS 173 B AND C10 IN LIGAND VMX 97 D
Sequence detailsCHAIN D IS COMPOSED AS UB/UBI-CYS-GLY-GLY-AVSN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop
Details: 22% PEG 2000 MME, 0.2 M di-ammonium tartrate, 3% EtGly, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.979
SYNCHROTRONAPS 24-ID-C20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 27, 2008
ADSC QUANTUM 3152CCDNov 9, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 33019 / % possible obs: 99 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.8
Reflection shellResolution: 2.6→2.67 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.7 / % possible all: 96.1

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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: 2.61→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.005 / SU ML: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.87 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1673 5.1 %RANDOM
Rwork0.227 ---
obs0.23 32957 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 99.51 Å2 / Biso mean: 22.961 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---2.72 Å20 Å2
3---2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.61→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 39 215 6978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226886
X-RAY DIFFRACTIONr_angle_refined_deg0.8971.9769296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.235848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97824.673306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.472151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9831539
X-RAY DIFFRACTIONr_chiral_restr0.0560.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215099
X-RAY DIFFRACTIONr_mcbond_it0.1811.54255
X-RAY DIFFRACTIONr_mcangle_it0.33726886
X-RAY DIFFRACTIONr_scbond_it0.35232631
X-RAY DIFFRACTIONr_scangle_it0.6054.52410
LS refinement shellResolution: 2.61→2.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 109 -
Rwork0.304 2159 -
all-2268 -
obs--93.49 %
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)
15.0818-0.16520.20295.745-1.23233.9066-0.4609-0.32280.70730.20590.26810.2464-0.63440.2150.19280.34140.05-0.25520.1787-0.03460.265923.15446.415.56
24.17441.07311.71645.8506-0.72912.6060.10240.0124-0.27970.00160.19350.12470.2072-0.09-0.29590.18490.0603-0.09880.1595-0.04770.079626.58320.13612.086
35.410.5387-2.98725.5348-2.8647.57180.3633-0.4868-0.18020.96750.51411.3318-0.2101-0.6634-0.87751.09210.05630.39720.96550.07820.710813.13728.56237.929
410.31174.63545.07518.15342.275612.57482.7499-2.5918-2.07983.2971-1.6615-1.79691.9406-1.5346-1.08832.0395-0.8726-1.24040.89160.72441.085938.1845.7439.63
512.8965.2578-0.59784.54080.14512.40350.3307-1.16040.98940.6364-0.4264-0.092-0.22940.53480.09570.4250.0023-0.10380.5743-0.11960.382248.93837.98622.036
63.00870.98171.14323.7772-0.61211.7305-0.2249-0.09160.27420.8895-0.212-1.1094-0.36280.54130.43680.4791-0.0083-0.42030.5693-0.00550.473848.93837.98622.036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 345
2X-RAY DIFFRACTION2B4 - 162
3X-RAY DIFFRACTION2B387 - 445
4X-RAY DIFFRACTION3B163 - 386
5X-RAY DIFFRACTION4B446 - 546
6X-RAY DIFFRACTION5D20 - 97
7X-RAY DIFFRACTION6A349 - 441
8X-RAY DIFFRACTION6B551 - 651
9X-RAY DIFFRACTION6D100 - 222

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