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- PDB-4npn: Crystal structure of human tetra-SUMO-2 -

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Basic information

Entry
Database: PDB / ID: 4npn
TitleCrystal structure of human tetra-SUMO-2
ComponentsSmall ubiquitin-related modifier 2
KeywordsPROTEIN TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation ...SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / SUMOylation of transcription factors / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / ubiquitin protein ligase binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
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 domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.633 Å
AuthorsKung, C.C.-H. / Naik, M.T. / Chen, C.L. / Ma, C. / Huang, T.H.
CitationJournal: Biochem.J. / Year: 2014
Title: Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.
Authors: Kung, C.C.-H. / Naik, M.T. / Wang, S.H. / Shih, H.M. / Chang, C.C. / Lin, L.Y. / Chen, C.L. / Ma, C. / Chang, C.F. / Huang, T.H.
History
DepositionNov 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small ubiquitin-related modifier 2


Theoretical massNumber of molelcules
Total (without water)11,4611
Polymers11,4611
Non-polymers00
Water52229
1
A: Small ubiquitin-related modifier 2

A: Small ubiquitin-related modifier 2

A: Small ubiquitin-related modifier 2

A: Small ubiquitin-related modifier 2


Theoretical massNumber of molelcules
Total (without water)45,8434
Polymers45,8434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_455x-1/3,y+1/3,z+1/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.123, 75.123, 33.116
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-108-

HOH

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Components

#1: Protein Small ubiquitin-related modifier 2 / SUMO-2 / HSMT3 / SMT3 homolog 2 / SUMO-3 / Sentrin-2 / Ubiquitin-like protein SMT3A / Smt3A


Mass: 11460.790 Da / Num. of mol.: 1 / Fragment: DELTAN11SUMO-2, UNP RESIDUES 12-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMT3A, SMT3H2, SUMO2, SUMO2 SMT3A SMT3H2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61956
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 0.1M Tris-HCl, 0.1M CHES, 30% PEG 600, pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Apr 20, 2012
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.63→30 Å / Num. obs: 8785 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 6.098 / Num. unique all: 875 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.633→23.206 Å / SU ML: 0.19 / σ(F): 1.98 / Phase error: 22.01 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 407 4.74 %RANDOM
Rwork0.1981 ---
all0.199 8661 --
obs0.199 8594 99.23 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.193 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2099 Å20 Å2-0 Å2
2--0.2099 Å20 Å2
3----0.4197 Å2
Refinement stepCycle: LAST / Resolution: 1.633→23.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms575 0 0 29 604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006584
X-RAY DIFFRACTIONf_angle_d1.087783
X-RAY DIFFRACTIONf_dihedral_angle_d15.959229
X-RAY DIFFRACTIONf_chiral_restr0.0885
X-RAY DIFFRACTIONf_plane_restr0.004104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6332-1.86950.26451280.2058275099
1.8695-2.35490.25111440.19252739100
2.3549-23.20860.19731350.1988269899
Refinement TLS params.Method: refined / Origin x: 12.8681 Å / Origin y: -5.2994 Å / Origin z: -5.3943 Å
111213212223313233
T0.0923 Å20.016 Å2-0.0003 Å2-0.1154 Å2-0.011 Å2--0.1006 Å2
L2.9954 °20.0864 °20.5171 °2-1.474 °20.0842 °2--1.3692 °2
S-0.004 Å °-0.1558 Å °-0.0247 Å °0.0424 Å °0.0282 Å °-0.0267 Å °0.1067 Å °0.1216 Å °0.0001 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESSEQ 17:87)

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