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- PDB-3ptf: X-ray structure of the non-covalent complex between UbcH5A and Ub... -

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Basic information

Entry
Database: PDB / ID: 3ptf
TitleX-ray structure of the non-covalent complex between UbcH5A and Ubiquitin
Components
  • Polyubiquitin-B
  • Ubiquitin-conjugating enzyme E2 D1
KeywordsLIGASE / protein-protein complex / E2 / ubiquitin / ubiquitin conjugating enzyme / alpha/beta
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 / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I ...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 / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / energy homeostasis / regulation of neuron apoptotic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / negative regulation of TORC1 signaling / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex
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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D1
Similarity search - Component
Biological speciesHomo sapiens (human)
Homo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBosanac, I. / Hymowitz, S.G.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Modulation of K11-Linkage Formation by Variable Loop Residues within UbcH5A.
Authors: Bosanac, I. / Phu, L. / Pan, B. / Zilberleyb, I. / Maurer, B. / Dixit, V.M. / Hymowitz, S.G. / Kirkpatrick, D.S.
History
DepositionDec 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D1
B: Ubiquitin-conjugating enzyme E2 D1
C: Polyubiquitin-B
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)52,2744
Polymers52,2744
Non-polymers00
Water72140
1
A: Ubiquitin-conjugating enzyme E2 D1
C: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)26,1372
Polymers26,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-9 kcal/mol
Surface area11730 Å2
MethodPISA
2
B: Ubiquitin-conjugating enzyme E2 D1
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)26,1372
Polymers26,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-7 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.462, 102.903, 159.806
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
21B
12C
22D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPROPRO1AA4 - 6110 - 67
21LYSLYSPROPRO1BB4 - 6110 - 67
12METMETLEULEU4CC1 - 734 - 76
22METMETLEULEU4DD1 - 734 - 76

NCS ensembles :
ID
1
2

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D1 / Stimulator of Fe transport / SFT / UBC4/5 homolog / UbcH5 / Ubiquitin carrier protein D1 / ...Stimulator of Fe transport / SFT / UBC4/5 homolog / UbcH5 / Ubiquitin carrier protein D1 / Ubiquitin-conjugating enzyme E2(17)KB 1 / Ubiquitin-conjugating enzyme E2-17 kDa 1 / Ubiquitin-protein ligase D1


Mass: 17277.756 Da / Num. of mol.: 2 / Fragment: E2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFT, UBC5A, UBCH5, UBCH5A, UBE2D1 / Plasmid: pet-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P51668, ubiquitin-protein ligase
#2: Protein Polyubiquitin-B


Mass: 8859.106 Da / Num. of mol.: 2 / Fragment: Ubiquitin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo Sapiens (human) / Gene: Ubiquitin / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P0CG47, UniProt: P0CG48*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of ...Details: Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 1, 2006
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 13165 / Num. obs: 13156 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 59 Å2 / Rsym value: 0.128 / Net I/σ(I): 17.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1309 / Rsym value: 0.458 / % possible all: 98.3

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 1X23

1ubq

1x23


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 30.479 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27538 622 4.8 %RANDOM
Rwork0.2087 ---
all0.21177 13247 --
obs0.21177 13133 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.342 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å2-0 Å20 Å2
2---1.82 Å2-0 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 0 40 3640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223698
X-RAY DIFFRACTIONr_bond_other_d0.0010.022549
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.9755023
X-RAY DIFFRACTIONr_angle_other_deg0.80836270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6495450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35224.753162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71915654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7391517
X-RAY DIFFRACTIONr_chiral_restr0.060.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02677
X-RAY DIFFRACTIONr_mcbond_it2.6192.52276
X-RAY DIFFRACTIONr_mcbond_other0.5052.5886
X-RAY DIFFRACTIONr_mcangle_it4.66153717
X-RAY DIFFRACTIONr_scbond_it3.5132.51422
X-RAY DIFFRACTIONr_scangle_it5.95151305
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A778tight positional0.020.05
22C990medium positional0.250.5
11A778tight thermal0.450.5
22C990medium thermal0.492
LS refinement shellResolution: 2.7→2.756 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.51 47 -
Rwork0.307 717 -
obs--98.58 %
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)
10.51650.05980.69241.40661.25313.21410.02640.029-0.02190.0688-0.0369-0.05570.2012-0.00780.01050.1293-0.00390.01440.08990.02680.08482.286319.046133.6864
21.02490.1941-0.08383.12620.05991.6981-0.2224-0.0511-0.0381-0.1340.2316-0.0582-0.03310.1883-0.00920.09660.01550.0260.1149-0.00370.078112.004950.291810.5067
31.9410.05940.84083.59830.12094.87860.08110.0728-0.02020.078-0.06980.0397-0.0654-0.0299-0.01120.0175-0.01270.02330.0461-0.00720.1027-0.613142.437233.0572
45.3677-0.9046-0.09595.2689-0.9294.93350.09060.11050.1599-0.0783-0.1136-0.1075-0.1206-0.14980.0230.1126-0.03220.03590.0710.01490.070510.337161.8829-10.3491
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 147
2X-RAY DIFFRACTION2B1 - 147
3X-RAY DIFFRACTION3C1 - 73
4X-RAY DIFFRACTION4D1 - 73

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