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- PDB-8suv: CHIP-TPR in complex with the C-terminus of CHIC2 -

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Basic information

Entry
Database: PDB / ID: 8suv
TitleCHIP-TPR in complex with the C-terminus of CHIC2
Components
  • Cysteine-rich hydrophobic domain-containing protein 2
  • E3 ubiquitin-protein ligase CHIP
KeywordsLIGASE / E3 ubiquitin ligase
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of mitophagy / ERBB2 signaling pathway / positive regulation of smooth muscle cell apoptotic process / nuclear inclusion body / misfolded protein binding / protein folding chaperone complex ...positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of mitophagy / ERBB2 signaling pathway / positive regulation of smooth muscle cell apoptotic process / nuclear inclusion body / misfolded protein binding / protein folding chaperone complex / cellular response to misfolded protein / ubiquitin-ubiquitin ligase activity / RIPK1-mediated regulated necrosis / Golgi-associated vesicle / chaperone-mediated autophagy / protein quality control for misfolded or incompletely synthesized proteins / TPR domain binding / SMAD binding / protein monoubiquitination / negative regulation of smooth muscle cell apoptotic process / R-SMAD binding / positive regulation of proteolysis / protein K63-linked ubiquitination / protein maturation / ERAD pathway / protein autoubiquitination / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / Hsp70 protein binding / heat shock protein binding / Downregulation of TGF-beta receptor signaling / positive regulation of protein ubiquitination / G protein-coupled receptor binding / response to ischemia / Regulation of TNFR1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / Hsp90 protein binding / RING-type E3 ubiquitin transferase / regulation of protein stability / tau protein binding / Regulation of necroptotic cell death / Downregulation of ERBB2 signaling / kinase binding / Z disc / Regulation of PTEN stability and activity / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / MAPK cascade / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cellular response to heat / protein-folding chaperone binding / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / intracellular membrane-bounded organelle / DNA repair / ubiquitin protein ligase binding / Golgi apparatus / enzyme binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cysteine-rich hydrophobic domain-containing protein 1/2 / Golgin subfamily A member 7/ERF4 / Golgin subfamily A member 7/ERF4 family / 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 ...Cysteine-rich hydrophobic domain-containing protein 1/2 / Golgin subfamily A member 7/ERF4 / Golgin subfamily A member 7/ERF4 family / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Cysteine-rich hydrophobic domain-containing protein 2 / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsCupo, A.R. / McDermott, L.E. / DeSilva, A.R. / Callahan, M. / Nix, J.C. / Gestwicki, J.E. / Page, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM128595 United States
CitationJournal: Biorxiv / Year: 2023
Title: Interaction with the membrane-anchored protein CHIC2 constrains the ubiquitin ligase activity of CHIP
Authors: Callahan, M. / Hodul, M. / Carroll, E. / Ravalin, M. / Nadel, C. / de Silva, A. / Cupo, A. / McDermott, L. / Nix, J. / Page, R. / Kao, A. / Gestwicki, J.
History
DepositionMay 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CHIP
B: E3 ubiquitin-protein ligase CHIP
C: E3 ubiquitin-protein ligase CHIP
D: E3 ubiquitin-protein ligase CHIP
F: Cysteine-rich hydrophobic domain-containing protein 2
G: Cysteine-rich hydrophobic domain-containing protein 2
H: Cysteine-rich hydrophobic domain-containing protein 2
I: Cysteine-rich hydrophobic domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,76712
Polymers69,3838
Non-polymers3844
Water7,278404
1
A: E3 ubiquitin-protein ligase CHIP
F: Cysteine-rich hydrophobic domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4423
Polymers17,3462
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-17 kcal/mol
Surface area7510 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase CHIP
G: Cysteine-rich hydrophobic domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)17,3462
Polymers17,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-8 kcal/mol
Surface area7620 Å2
MethodPISA
3
C: E3 ubiquitin-protein ligase CHIP
H: Cysteine-rich hydrophobic domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5384
Polymers17,3462
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-26 kcal/mol
Surface area7480 Å2
MethodPISA
4
D: E3 ubiquitin-protein ligase CHIP
I: Cysteine-rich hydrophobic domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4423
Polymers17,3462
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-18 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.526, 82.356, 78.394
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
E3 ubiquitin-protein ligase CHIP / Antigen NY-CO-7 / CLL-associated antigen KW-8 / Carboxy terminus of Hsp70-interacting protein / ...Antigen NY-CO-7 / CLL-associated antigen KW-8 / Carboxy terminus of Hsp70-interacting protein / RING-type E3 ubiquitin transferase CHIP / STIP1 homology and U box-containing protein 1


Mass: 15884.057 Da / Num. of mol.: 4 / Fragment: TPR domain, residues 21-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STUB1, CHIP, PP1131 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UNE7, RING-type E3 ubiquitin transferase
#2: Protein/peptide
Cysteine-rich hydrophobic domain-containing protein 2 / BrX-like translocated in leukemia


Mass: 1461.702 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UKJ5
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M Magnesium sulfate heptahydrate, 0.1 M HEPES, 28 % v/v PEG Smear Medium

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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
RadiationMonochromator: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.63→46.53 Å / Num. obs: 71293 / % possible obs: 96.37 % / Redundancy: 7 % / Biso Wilson estimate: 20.64 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1491 / Rpim(I) all: 0.06058 / Rrim(I) all: 0.1612 / Net I/σ(I): 8.52
Reflection shellResolution: 1.63→1.688 Å / Redundancy: 7.2 % / Rmerge(I) obs: 2.287 / Mean I/σ(I) obs: 0.88 / Num. unique obs: 50246 / CC1/2: 0.652 / CC star: 0.888 / Rpim(I) all: 0.9115 / Rrim(I) all: 2.465 / % possible all: 94.59

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS0.95data reduction
XSCALEdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→46.53 Å / SU ML: 0.2829 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2903 3017 2.17 %
Rwork0.2741 136121 -
obs0.2744 71293 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.37 Å2
Refinement stepCycle: LAST / Resolution: 1.63→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 20 404 4807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01224497
X-RAY DIFFRACTIONf_angle_d1.55016066
X-RAY DIFFRACTIONf_chiral_restr0.0923637
X-RAY DIFFRACTIONf_plane_restr0.0058802
X-RAY DIFFRACTIONf_dihedral_angle_d13.94451723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.660.44931270.45686057X-RAY DIFFRACTION92.34
1.66-1.680.40661160.45585955X-RAY DIFFRACTION92.05
1.68-1.710.47461570.4366006X-RAY DIFFRACTION93.39
1.71-1.740.34851100.42096062X-RAY DIFFRACTION94
1.74-1.780.42071460.4086079X-RAY DIFFRACTION94.36
1.78-1.810.39631190.39636049X-RAY DIFFRACTION93.4
1.81-1.850.35861690.38416130X-RAY DIFFRACTION94.96
1.85-1.90.35171140.36446173X-RAY DIFFRACTION95.68
1.9-1.940.41371250.38856215X-RAY DIFFRACTION95.87
1.94-1.990.33831420.35686226X-RAY DIFFRACTION96.54
1.99-2.050.31400.34346248X-RAY DIFFRACTION96.48
2.05-2.120.35541450.2976219X-RAY DIFFRACTION96.18
2.12-2.20.33331470.29486233X-RAY DIFFRACTION96.56
2.2-2.280.41831260.29756220X-RAY DIFFRACTION96.62
2.28-2.390.26551400.27936209X-RAY DIFFRACTION96.92
2.39-2.510.25881470.2686285X-RAY DIFFRACTION96.9
2.51-2.670.36811290.27886314X-RAY DIFFRACTION97.05
2.67-2.880.30491530.2596278X-RAY DIFFRACTION97.75
2.88-3.170.24231470.25556342X-RAY DIFFRACTION97.92
3.17-3.620.23321390.21536311X-RAY DIFFRACTION97.71
3.62-4.570.20731480.18866218X-RAY DIFFRACTION96.22
4.57-46.530.25261310.21116292X-RAY DIFFRACTION97.53
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)
13.663220287520.727030576202-2.359771252552.00421608719-0.3447407713142.966726999550.2493976470470.3938957861650.319325035554-0.0690815164318-0.07838283703240.162485734097-0.256529556304-0.177355265524-0.1489808856950.1695267956240.02045651595970.01782708122640.695253449129-0.100618699210.162843773928-25.138-2.474-59.068
22.124523301580.0235220396504-1.137124329344.1560431272-1.440361909554.825435156350.06609127164690.3408984108380.0760024163902-0.477725165146-0.0348686110662-0.08994628899560.223103870529-0.0983911497988-0.007047560710830.1611269266860.01483831112050.003070512840030.628406424256-0.1067881215390.174323538807-23.657-4.836-67.039
32.33263225630.0299418492205-0.08898605471950.490636947203-1.021614112692.478456966220.002690180843870.0628953440544-0.0736932025397-0.0780944051428-0.0303872946581-0.0581639326750.2044202352030.2728495377430.05044639977710.1566978257350.0007694216430320.02358224323440.354668597941-0.09035132388370.1634363990028.58-10.309-3.978
42.72103146025-0.231283533672-1.475346508290.9779629735490.09339345526812.551788530070.112350991445-0.2383442294040.1495947853760.119994460154-0.05654337210630.0141350932284-0.1040964386660.0643279265425-0.05770340392690.164484744136-0.03394461354580.03016000025510.6468860214710.003699382737370.188123620772-5.025-3.9039.396
56.19853439619-1.45646352445.753516847654.15359597561-3.480789171686.52944857506-0.0963737092252-0.02145240724990.452429161398-0.215109658820.295046720085-0.0310152029964-0.477097709812-0.123309973777-0.1864351538410.230736519778-0.05304735600370.02163139230840.342630922383-0.01759347889250.181757934616-22.2077.177-19.755
63.97463162736-2.602345501582.356972021036.52840931072-2.669672643928.15185216857-0.193480108947-0.2517083560540.646531433430.5893586769340.267405364343-0.863560248901-1.07144873360.632563111735-0.06714050673260.377233050391-0.1412336599990.01478133122450.738216798987-0.1682349329740.345787702188-7.3087.147-32.858
77.792058058993.83762962416-1.774726067385.1228085776-5.86455679632.00001926084-0.2032826237950.0325275682437-0.50106967844-0.4482789121940.0340895504598-0.3453226967930.7675149373340.4792858632580.1757869691630.228296702182-0.01850036689320.03092304555570.618166415775-0.07600941801030.193020796973-32.086-15.206-58.798
82.99950157895-1.332836878160.7422185887073.977968993223.149204570864.937732730520.0449754398442-0.159409558995-0.5289056378390.1994989544980.05503555264510.2629640600160.526109444946-0.199482321511-0.08118034088510.431596041816-0.0288457142539-0.03348712032980.013318608271-0.08840658771930.3903614871061.482-16.3336.251
92.605752283010.3395493256980.08247397984711.63784654536-1.343075545812.906932304190.067240496033-0.1024150826610.03003022782040.09637292232780.0468909584689-0.0442925512489-0.1733052894570.0551134833126-0.1064758272170.15126341611-0.00544722657606-0.009481752015640.413859123956-0.08521561354620.162848023223-14.6460.644-9.95
101.993562019650.3186888241740.6099426634061.05819954017-0.5388700917452.027398665420.03259355813640.24368452079-0.124367170719-0.163221261970.06656076542880.04787114223920.2139345688770.128373206079-0.1018503604230.1586986104960.004775653342-0.01833269306360.674831935019-0.004991866544080.192376827053-28.23-5.844-23.445
111.820270394150.185854343089-0.04744323839410.4641268966660.4386494689871.01781569338-0.03021828313440.1701516164980.116478767373-0.01678902325180.002222478458010.0894340007356-0.214030387694-0.02533916974860.08671567273070.171789948236-0.00603649034384-0.03426432770710.741635912336-0.09090040565060.194962362911-15.0970.653-42.974
121.888911213070.1330121053460.6003406209680.638339908650.3206022401511.680946408970.123048742187-0.401414196944-0.1699754228450.205093721992-0.03423785018650.01065059122670.151772290403-0.092586014767-0.001138372339070.178103711929-0.113986659721-0.0624689037751.00255171011-0.1372960812080.124007206974-1.413-6.11-29.813
132.63517647118-0.426078496090.08045558720620.9024585140080.415015835052.43288451946-0.0786702426897-0.269482729579-0.5000494504230.04977892019160.07115496280730.1009812474830.2955488745970.132224484920.08480430149150.1571796765380.01688646882760.05470544189380.766109094232-0.004165375165780.263084145308-42.9-16.028-48.642
141.601083018960.03564975275920.2990136992880.256559367710.1447570260080.615638750308-0.0211950432041-0.2535876300880.006944288389850.00674329106170.01011504311180.0495521217906-0.05986538597950.109741094498-0.01326710403690.0820045066599-0.03291746495410.08600299471140.797187533538-0.09836853854350.147330816741-34.712-5.383-49.861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 94:126 )C94 - 126
2X-RAY DIFFRACTION2( CHAIN C AND RESID 127:150 )C127 - 150
3X-RAY DIFFRACTION3( CHAIN D AND RESID 23:93 )D23 - 93
4X-RAY DIFFRACTION4( CHAIN D AND RESID 94:150 )D94 - 150
5X-RAY DIFFRACTION5( CHAIN F AND RESID 157:165 )F157 - 165
6X-RAY DIFFRACTION6( CHAIN G AND RESID 157:165 )G157 - 165
7X-RAY DIFFRACTION7( CHAIN H AND RESID 159:165 )H159 - 165
8X-RAY DIFFRACTION8( CHAIN I AND RESID 158:165 )I158 - 165
9X-RAY DIFFRACTION9( CHAIN A AND RESID 23:93 )A23 - 93
10X-RAY DIFFRACTION10( CHAIN A AND RESID 94:150 )A94 - 150
11X-RAY DIFFRACTION11( CHAIN B AND RESID 23:93 )B23 - 93
12X-RAY DIFFRACTION12( CHAIN B AND RESID 94:150 )B94 - 150
13X-RAY DIFFRACTION13( CHAIN C AND RESID 23:55 )C23 - 55
14X-RAY DIFFRACTION14( CHAIN C AND RESID 56:93 )C56 - 93

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