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- PDB-2c4p: Crystal structure of human ubiquitin-conjugating enzyme UbcH5A -

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Basic information

Entry
Database: PDB / ID: 2c4p
TitleCrystal structure of human ubiquitin-conjugating enzyme UbcH5A
ComponentsUBIQUITIN-CONJUGATING ENZYME E2 D1
KeywordsLIGASE / THIOESTERIFICATION / UBIQUITIN-CONJUGATING ENZYME / UBL CONJUGATION PATHWAY
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / Signaling by BMP / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity ...positive regulation of protein polyubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / Signaling by BMP / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / negative regulation of BMP signaling pathway / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / ubiquitin ligase complex / negative regulation of TORC1 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / Separation of Sister Chromatids / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Ovarian tumor domain proteases / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDodd, R.B. / Read, R.J.
CitationJournal: To be Published
Title: Structures of Two Human Ubiquitin-Conjugating Enzymes from Twinned Crystals
Authors: Dodd, R.B. / Read, R.J.
History
DepositionOct 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2 D1
B: UBIQUITIN-CONJUGATING ENZYME E2 D1


Theoretical massNumber of molelcules
Total (without water)37,3892
Polymers37,3892
Non-polymers00
Water2,072115
1
A: UBIQUITIN-CONJUGATING ENZYME E2 D1


Theoretical massNumber of molelcules
Total (without water)18,6941
Polymers18,6941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: UBIQUITIN-CONJUGATING ENZYME E2 D1


Theoretical massNumber of molelcules
Total (without water)18,6941
Polymers18,6941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.621, 50.565, 66.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99647, -0.08301, 0.01224), (-0.08344, -0.99571, 0.03994), (0.00887, -0.04082, -0.99913)
Vector: -21.35963, 83.07368, 33.71801)

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2 D1 / UBIQUITIN-PROTEIN LIGASE D1 / UBIQUITIN CARRIER PROTEIN D1 / UBCH5 / UBIQUITIN-CONJUGATING ENZYME ...UBIQUITIN-PROTEIN LIGASE D1 / UBIQUITIN CARRIER PROTEIN D1 / UBCH5 / UBIQUITIN-CONJUGATING ENZYME E2-17KDA / UBCH5A


Mass: 18694.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-12 (EMBL) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P51668, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE COVALENT ATTACHMENT OF UBIQUITIN TO OTHER PROTEINS. MEDIATES THE SELECTIVE ...CATALYZES THE COVALENT ATTACHMENT OF UBIQUITIN TO OTHER PROTEINS. MEDIATES THE SELECTIVE DEGRADATION OF SHORT-LIVED AND ABNORMAL PROTEINS. FUNCTIONS IN THE E6/E6-AP-INDUCED UBIQUITINATION OF P53/TP53.
Sequence detailsRESIDUES FOR WHICH INSUFFICIENT DENSITY WAS OBSERVED FOR SIDECHAINS WERE TRUNCATED TO ALANINES. THE ...RESIDUES FOR WHICH INSUFFICIENT DENSITY WAS OBSERVED FOR SIDECHAINS WERE TRUNCATED TO ALANINES. THE PROTEIN WAS TAGGED WITH A HIS6-TAG THAT WAS NEVER CLEAVED FROM THE PROTEIN. THEREFORE, IN ADDITION TO THE RGS SEQUENCE PRECEDING THE UNIPROT UBCH5A SEQUENCE, THE FOLLOWING RESIDUES WERE PRESENT IN THE STRUCTURE, BUT NOT LOCATED IN THE ELECTRON DENSITY MAPS,PRESUMABLY DUE TO DISORDER: MKHHHHHHPMSGLVP

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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 Å3/Da / Density % sol: 39 %
Description: DATA WERE INITIALLY SOLVED IN P1 TO ALLOW DISTINCTION BETWEEN CRYSTALLOGRAPHIC AND PSEUDOSYMMETRY AXES TO BE MADE PRIOR TO PROCESSING IN P21.
Crystal growpH: 4.6
Details: 200 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9821
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 7, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9821 Å / Relative weight: 1
ReflectionResolution: 2.35→30.15 Å / Num. obs: 89448 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 2.35→2.47 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 87.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QCQ

1qcq


Resolution: 2.35→30.14 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1012047.88 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TWIN_LSQ
Details: DUE TO THE PRESENCE OF ORTHORHOMBIC PSEUDOSYMMETRY, THE TEST SET OF REFLECTIONS WERE CHOSEN IN P212121 AND THEN EXPANDED TO COVER THE MONOCLINIC SPACE GROUP. DATA WERE FOUND TO BE NEAR- ...Details: DUE TO THE PRESENCE OF ORTHORHOMBIC PSEUDOSYMMETRY, THE TEST SET OF REFLECTIONS WERE CHOSEN IN P212121 AND THEN EXPANDED TO COVER THE MONOCLINIC SPACE GROUP. DATA WERE FOUND TO BE NEAR- PERFECTLY TWINNED AND WERE THEREFORE TREATED AS PERFECTLY TWINNED. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT WITH POSITIONAL RESTRAINTS OF 30 KCAL/MOL-A**2 (300 INITIALLY) AND B-FACTOR TARGET SIGMA OF 2
RfactorNum. reflection% reflectionSelection details
Rfree0.272 878 7.4 %RANDOM
Rwork0.232 ---
obs0.232 11589 96.8 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 76.0135 Å2 / ksol: 0.358298 e/Å3
Displacement parametersBiso mean: 48.06 Å2
Baniso -1Baniso -2Baniso -3
1--5.05 Å20 Å20 Å2
2--1.29 Å20 Å2
3---3.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 2.35→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 0 115 2458
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.371
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it1.32
X-RAY DIFFRACTIONc_scangle_it2.072.5
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.408 87 6.6 %
Rwork0.335 1228 -
obs--97.31 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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