[English] 日本語
Yorodumi
- PDB-9ye9: Structure of UbcH5b in complex with the U-box domain of the E3 ub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ye9
TitleStructure of UbcH5b in complex with the U-box domain of the E3 ubiquitin ligase CHIP
Components
  • E3 ubiquitin-protein ligase CHIP
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / Ubiquitin conjugating enzyme / ubiquitin ligase
Function / homology
Function and homology information


cerebellar Purkinje cell layer structural organization / regulation of glucocorticoid metabolic process / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / TPR domain binding / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Hsp70 protein binding / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...cerebellar Purkinje cell layer structural organization / regulation of glucocorticoid metabolic process / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / TPR domain binding / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Hsp70 protein binding / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Hsp90 protein binding / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein modification process / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA repair / signal transduction / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / E3 ubiquitin-protein ligase CHIP / Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHomo sapiens (human)
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsManage, M.M. / Nix, J.C. / Page, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128595 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Functional and structural analyses of UbcH5 mutants with enhanced binding to the E3 ubiquitin ligase CHIP
Authors: Manage, M.M. / Nix, J.C. / Page, R.C.
History
DepositionSep 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
B: E3 ubiquitin-protein ligase CHIP
C: E3 ubiquitin-protein ligase CHIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,43310
Polymers36,9713
Non-polymers4627
Water2,576143
1
B: E3 ubiquitin-protein ligase CHIP
C: E3 ubiquitin-protein ligase CHIP
hetero molecules

A: Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,43310
Polymers36,9713
Non-polymers4627
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area3810 Å2
ΔGint-50 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.081, 59.138, 112.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 17182.707 Da / Num. of mol.: 1 / Mutation: M1K, C85K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Protein E3 ubiquitin-protein ligase CHIP / RING-type E3 ubiquitin transferase CHIP / STIP1 homology and U box-containing protein 1


Mass: 9894.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: stub1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F6NGW2, RING-type E3 ubiquitin transferase
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Magnesium chloride hexahydrate, 0.1 M Potassium chloride, 0.1 M PIPES, 20 % v/v PEG Smear Medium

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00002 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.01→41.44 Å / Num. obs: 46470 / % possible obs: 94.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 34.56 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.1597 / Rpim(I) all: 0.105 / Rrim(I) all: 0.1921 / Net I/σ(I): 3.65
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2619 / CC1/2: 0.407 / Rpim(I) all: 0.81 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→41.44 Å / SU ML: 0.3995 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.2146
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2881 3520 7.57 %
Rwork0.2415 42950 -
obs0.245 46470 92.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.46 Å2
Refinement stepCycle: LAST / Resolution: 2.01→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 22 143 2495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922405
X-RAY DIFFRACTIONf_angle_d1.04493260
X-RAY DIFFRACTIONf_chiral_restr0.06357
X-RAY DIFFRACTIONf_plane_restr0.0109427
X-RAY DIFFRACTIONf_dihedral_angle_d15.8908911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.040.48341470.40621814X-RAY DIFFRACTION96.98
2.04-2.070.38771450.37921805X-RAY DIFFRACTION97.7
2.07-2.10.36141530.37091835X-RAY DIFFRACTION99.15
2.1-2.130.40541460.3591838X-RAY DIFFRACTION99.15
2.13-2.170.35191620.34591812X-RAY DIFFRACTION99.15
2.17-2.20.47381500.4191729X-RAY DIFFRACTION93.25
2.2-2.240.5951470.488699X-RAY DIFFRACTION38.06
2.25-2.290.4195510.5144637X-RAY DIFFRACTION38.07
2.29-2.330.48221430.38471604X-RAY DIFFRACTION86.27
2.33-2.380.41251430.31021824X-RAY DIFFRACTION99.7
2.38-2.440.3511510.30351848X-RAY DIFFRACTION98.96
2.44-2.50.30981480.2941840X-RAY DIFFRACTION99.35
2.5-2.570.33121470.26871819X-RAY DIFFRACTION99.54
2.57-2.640.33711510.26241852X-RAY DIFFRACTION99.6
2.64-2.730.34441470.2691830X-RAY DIFFRACTION99.7
2.73-2.830.34611570.26251857X-RAY DIFFRACTION99.6
2.83-2.940.3431570.26281817X-RAY DIFFRACTION99.2
2.94-3.070.3471520.23731839X-RAY DIFFRACTION99.15
3.07-3.230.29051430.23461838X-RAY DIFFRACTION99.4
3.23-3.440.25171490.22061831X-RAY DIFFRACTION99.1
3.44-3.70.33961380.24991731X-RAY DIFFRACTION93.4
3.7-4.070.20551440.19961725X-RAY DIFFRACTION93.64
4.07-4.660.20551460.16481844X-RAY DIFFRACTION99.85
4.66-5.870.20391570.17331835X-RAY DIFFRACTION99.35
5.87-41.440.20341460.16651847X-RAY DIFFRACTION99.8
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)
18.77600430126-3.134958665831.270736250275.7569030138-1.533012083073.212842418450.6095046271520.192996133877-0.431419443482-0.339761118576-0.2034111315130.2751094346630.469615134829-0.101292248093-0.4150858247460.381126998358-0.0903697635856-0.09537891676230.515531869124-0.01999308191670.316393260162-17.3364478213-27.88358761610.7418212325
26.743895352350.2598078069775.991632625017.85272797244-0.3727602163617.714857516730.3962682018461.904540573710.347892394602-0.522889976347-0.0890859895206-0.4980869623950.3190587660231.48015193653-0.2863383413780.5268456143890.0605761118062-0.1394621280490.500229228431-0.01005331862930.403496091746-5.08134583027-33.219294985818.9800776538
35.846631333450.2852419858895.352157455653.06491630128-0.02085676671616.071919608240.263675413005-0.346144336957-0.5395917583090.2167370257850.261366261433-0.1994370573520.334922513176-0.522625557753-0.4887440759840.4036613903480.0172892878046-0.03548180248960.2832045399040.03933863524470.235701640391-6.1551033924-27.297401039325.6866235381
43.538405997310.07329504825272.455354209281.552971689740.1845314254967.34734628644-0.100661636368-0.2411094226760.06522912009870.3779404719910.246175688619-0.10193499591-0.390049965863-0.090792856994-0.1305835763170.2558261000390.02873693645690.002916954379560.149435812271-0.0002912234343290.21775760384-7.99601917661-17.254402280224.0959416932
57.48223680952.7949523235.25379631153.690166250793.972381228775.53398182108-0.5930716549690.3856982839830.529702004254-0.3262777430890.478915302855-0.309164015162-1.245537909570.8208896075150.1214988800380.374654411854-0.0573484739991-0.05907689865660.2839234257470.04178447744520.257656613309-6.1812900646-14.212253020713.9854274032
67.035674615193.207957684466.894922872515.736396373093.312219313539.400426080230.3473376708450.645409946868-0.8499302341910.5249565153390.230449225258-0.4742059021581.176772952981.19368100678-0.5156088179770.3444850068140.115534851303-0.008634722449540.245774185032-0.009320106051850.317589820904-0.358015066938-22.487440264518.479009354
78.620133082780.4649782818530.5696750508664.889181242960.7711891759342.85215957182-0.4499860955970.9383309326490.420098589395-0.4408884429490.284610381912-0.00778616751551-0.4186909689810.1979279211240.1242960335580.325600231092-0.0273460817372-0.1234338154810.334806735213-0.02040896542140.2987834508028.11679692877-9.9389503857828.7247777793
89.01562740953.16923117524-0.214144079456.0732924893-0.6127557420360.7311663252430.62114543628-0.615282895927-0.4028932051361.28785277059-0.433519162584-0.7651531204120.02064070706990.158104587916-0.1370603216930.5747309524230.0595739467639-0.2019011918810.279760465150.001026235891160.4036291138598.16178124267-21.775506561436.5223718705
93.18215714913-2.166435794272.969285636763.33211939903-3.800772171424.47508332443-0.151437002433-1.70335213358-2.70255113128-1.018143443330.186719075974-2.403961141742.96860725213-0.344779892646-0.08651276689750.8799193559560.00561261756121-0.0585970851790.6972860709730.1889002825691.10491647973-10.4233753042-32.5817165417-3.28478941267
106.70692508651.020741148553.966298613567.513736898611.853412328487.323783131610.139351377560.771981864042-1.221483136670.191994583157-0.120093230010.2329461949871.5084299392-0.526864424085-0.03761545511430.472862429317-0.1371574320870.0729341981120.532627726247-0.1244457151670.43914560645-15.4594466198-24.5373625115-1.5582396914
112.19726382901-0.186746289552.585086073023.46092869762.559304583695.438064819560.02889640830940.217214088463-0.1600185751460.395504733288-0.02890489035020.2193687644940.0279230273811-0.1407407762070.04960113771930.372896382852-0.1104472739650.01402318718850.6632756974430.06494979500820.261451134009-7.60395178741-15.9944891877-7.06801721927
123.907929793762.00920861334-3.644374616478.29785875282.072844501246.688695568390.2104096762730.03994988058910.00565181602508-0.1108854672380.02293634099860.707593233861-0.155409394331-1.34512461573-0.1661237249570.2475190953210.0375576420820.02068849677640.5450803668760.08916729322240.249140496179-16.3816204217-14.3319865959-0.321768424212
134.41865324549-0.5918204845860.1392499821374.741727832322.298559397762.33146932869-0.006519865287910.5991491369910.265922215718-0.2261031522720.117205177606-0.0263675222804-0.4284681420450.0597118576822-0.1395434218660.299559049346-0.02368519768750.04354203529840.3406730354470.06243215686630.191821474418-8.94167480103-10.432065493-2.37295081994
142.61343673189-0.2805074701691.259540694620.663306891639-0.2870239095770.642434222434-0.01726147214991.08419357018-1.18460303552-0.3331672802630.1648996811120.3047400732170.966667101717-0.504888843905-0.3959284881090.632941069655-0.368627914350.07051596890440.807537744287-0.3645745033450.645031890294-15.6461282046-30.2401578388-12.8785771412
153.136609861710.271605181398-1.451866710454.08786425506-3.877032636064.135647557850.1193175972810.890792849078-0.785832720499-1.3190211088-0.4182769564210.01791089358921.89942776351-0.1679121058840.2071152605810.749263427921-0.05570586835280.05068700556850.821278839443-0.2101858793840.532655144548-2.60749958248-27.7064179026-21.7508843903
162.320728704613.08807416246-2.098287027034.44228848405-1.491875017036.87747417181-0.1992381378761.032590181370.0401659851217-0.557433223928-0.250944441863-0.0472667081450.33779642297-0.1367187714920.4624504358190.3604936133950.05255167712140.04784630146310.8020826498940.03962213440120.345942245644-1.54768612717-14.0209141935-21.6482874761
174.87608683427-1.568955446992.817968580646.456846601813.769401765065.30105105675-0.2759819916360.618608261461-1.43497264265-0.429430096350.326288224544-0.2900768141751.726335469660.367368034605-0.07131126572470.832335466083-0.07468839595880.2641353941650.490119315326-0.1700700491050.595266052159-2.23318139584-31.6899033522-11.1875272157
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -4 through 15 )AA-4 - 151 - 20
22chain 'A' and (resid 16 through 25 )AA16 - 2521 - 30
33chain 'A' and (resid 26 through 55 )AA26 - 5531 - 60
44chain 'A' and (resid 56 through 84 )AA56 - 8461 - 89
55chain 'A' and (resid 85 through 98 )AA85 - 9890 - 103
66chain 'A' and (resid 99 through 111 )AA99 - 111104 - 116
77chain 'A' and (resid 112 through 130 )AA112 - 130117 - 135
88chain 'A' and (resid 131 through 147 )AA131 - 147136 - 152
99chain 'B' and (resid 207 through 212 )BE207 - 2121 - 6
1010chain 'B' and (resid 213 through 223 )BE213 - 2237 - 17
1111chain 'B' and (resid 224 through 231 )BE224 - 23118 - 25
1212chain 'B' and (resid 232 through 244 )BE232 - 24426 - 38
1313chain 'B' and (resid 245 through 264 )BE245 - 26439 - 58
1414chain 'B' and (resid 265 through 278 )BE265 - 27859 - 72
1515chain 'C' and (resid 209 through 223 )CF209 - 2231 - 15
1616chain 'C' and (resid 224 through 264 )CF224 - 26416 - 56
1717chain 'C' and (resid 265 through 277 )CF265 - 27757 - 69

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more