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- PDB-5c1b: p97-delta709-728 in complex with a UFD1-SHP peptide -

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Basic information

Entry
Database: PDB / ID: 5c1b
Titlep97-delta709-728 in complex with a UFD1-SHP peptide
Components
  • Transitional endoplasmic reticulum ATPase
  • Ubiquitin fusion degradation protein 1 homolog
KeywordsHYDROLASE / AAA ATPase / ERAD / VCP / CDC48
Function / homology
Function and homology information


UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion ...UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / NADH metabolic process / regulation of protein localization to chromatin / vesicle-fusing ATPase / cellular response to misfolded protein / : / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / ERAD pathway / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / negative regulation of type I interferon production / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / Protein methylation / negative regulation of smoothened signaling pathway / interstrand cross-link repair / Attachment and Entry / : / ATP metabolic process / endoplasmic reticulum unfolded protein response / proteasome complex / lipid droplet / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / skeletal system development / ADP binding / proteasomal protein catabolic process / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / Translesion Synthesis by POLH / ABC-family proteins mediated transport / establishment of protein localization / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / cellular response to heat / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / regulation of apoptotic process / secretory granule lumen / cysteine-type deubiquitinase activity / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / Ub-specific processing proteases / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / glutamatergic synapse / lipid binding / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation
Similarity search - Function
Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / Ubiquitin fusion degradation protein UFD1 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain ...Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / Ubiquitin fusion degradation protein UFD1 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Transitional endoplasmic reticulum ATPase / Ubiquitin recognition factor in ER-associated degradation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.08 Å
AuthorsHaenzelmann, P. / Schindelin, H.
CitationJournal: Structure / Year: 2016
Title: Characterization of an Additional Binding Surface on the p97 N-Terminal Domain Involved in Bipartite Cofactor Interactions.
Authors: Hanzelmann, P. / Schindelin, H.
History
DepositionJun 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
V: Ubiquitin fusion degradation protein 1 homolog
U: Ubiquitin fusion degradation protein 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)532,93940
Polymers525,9718
Non-polymers6,96832
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59670 Å2
ΔGint-405 kcal/mol
Surface area176050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.715, 180.664, 254.958
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFVU

#1: Protein
Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 86933.094 Da / Num. of mol.: 6 / Mutation: 709-728 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein/peptide Ubiquitin fusion degradation protein 1 homolog / UB fusion protein 1


Mass: 2186.454 Da / Num. of mol.: 2 / Fragment: UNP residues 221-241 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92890

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Non-polymers , 5 types, 62 molecules

#3: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 6.5-7% PEG 4000, 0.4-0.6 M potassium acetate, 0.1 M MES pH 5.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.08→49.14 Å / Num. obs: 120596 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 106.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.037 / Net I/σ(I): 12.8 / Num. measured all: 1326505
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.08-3.1310.92.5821.16437259200.5270.81399.9
16.87-49.149.90.04240.681708220.9990.01396.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.1.27data scaling
MxCuBEdata collection
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CF3

3cf3


Resolution: 3.08→49.136 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 6052 5.02 %
Rwork0.1975 114426 -
obs0.1997 120478 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 575.3 Å2 / Biso mean: 145.5665 Å2 / Biso min: 45.47 Å2
Refinement stepCycle: final / Resolution: 3.08→49.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34227 0 574 30 34831
Biso mean--111.54 126.68 -
Num. residues----4365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335264
X-RAY DIFFRACTIONf_angle_d0.7347648
X-RAY DIFFRACTIONf_chiral_restr0.045335
X-RAY DIFFRACTIONf_plane_restr0.0036232
X-RAY DIFFRACTIONf_dihedral_angle_d17.06513669
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.08-3.1150.3442280.315237643992
3.115-3.15170.35521950.304337573952
3.1517-3.19010.38581930.284337843977
3.1901-3.23050.32141990.272537823981
3.2305-3.2730.29662020.260237723974
3.273-3.31780.29852060.251137403946
3.3178-3.36520.31391950.239538274022
3.3652-3.41540.29911830.248837743957
3.4154-3.46870.2941800.24537883968
3.4687-3.52560.30652030.226937913994
3.5256-3.58640.25142090.220937513960
3.5864-3.65160.29391800.208438103990
3.6516-3.72180.27751790.220438284007
3.7218-3.79770.25492180.214437623980
3.7977-3.88030.27242070.205637843991
3.8803-3.97050.2561940.194737813975
3.9705-4.06970.22372140.187737874001
4.0697-4.17970.23872120.184138254037
4.1797-4.30260.24492040.18937913995
4.3026-4.44140.22462080.17737823990
4.4414-4.60010.23972090.173238104019
4.6001-4.78410.21361920.170538344026
4.7841-5.00160.22831950.175338384033
5.0016-5.2650.20971880.184338244012
5.265-5.59450.2552220.204438474069
5.5945-6.02570.26491840.217238614045
6.0257-6.63080.25042110.209338494060
6.6308-7.58730.24832000.194438944094
7.5873-9.54770.17962070.157839384145
9.5477-49.14210.20842350.192140514286
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)
14.0973-2.16370.53934.6444-0.42124.72080.12470.48650.52230.2391-0.08810.97680.2227-1.4896-0.00270.7897-0.13260.211.7338-0.03781.5091-52.24786.032361.7124
26.60762.9840.93553.51321.50785.46960.3537-0.56930.00810.4541-0.40510.27460.2567-0.2560.0580.5857-0.02870.06690.73750.15930.7663-22.22766.444361.2616
31.6537-1.19640.29451.6906-1.01312.0702-0.0910.1588-0.1813-0.20840.13410.33210.5152-0.5189-0.05850.9337-0.251-0.03410.78620.10040.8894-15.3548-27.159852.1903
43.2653-0.9532.01571.1863-0.41425.59860.05650.45260.3134-0.5792-0.12490.4314-0.1325-0.68070.06690.9063-0.0037-0.17070.9910.24430.9981-25.27919.099614.4689
54.3399-0.2824-1.18131.7167-0.15236.46690.12960.42510.0301-0.2958-0.0811-0.06490.6903-0.3176-0.11030.6440.064-0.00270.54390.18620.718-7.396613.104224.8685
62.3857-0.185-0.56461.6915-0.27161.8681-0.13590.5625-0.3346-0.13110-0.00190.452-0.2170.11630.9887-0.1780.02250.82190.00110.6444-0.9251-21.026222.5352
71.49271.3519-1.7142.1628-2.77195.103-0.16550.40990.146-0.8147-0.1267-0.40620.02490.19350.26111.04150.02910.16890.79890.20580.8826.154633.0457.5312
84.0784-0.2231-0.78182.3842-0.71043.9677-0.1290.1533-0.3879-0.2009-0.2522-0.56320.23140.60550.34880.67290.08480.06840.59110.15420.692526.81221.460425.7349
93.57310.35860.31092.1915-0.27841.12060.10510.7733-0.1685-0.23960.0422-0.52710.35020.471-0.13480.990.09560.17171.055-0.03320.888531.8881-11.896419.7773
103.3380.96273.04296.65852.04884.9373-0.0069-0.11590.4434-0.2276-0.1285-0.7854-0.74420.73380.12761.1244-0.4080.0451.03480.14821.56967.661338.758251.8272
115.591-0.75280.72451.9672-1.2875.48590.1990.4520.0241-0.1228-0.3245-0.4557-0.27470.20960.11280.6503-0.0887-0.01180.55170.10980.916939.403625.092647.3101
121.73880.69140.00022.22060.18491.85340.1845-0.1066-0.26190.0011-0.2913-0.7070.17960.53780.10550.59280.0518-0.01591.01350.21781.170352.2139-6.682751.1382
132.7024-0.20412.04180.6084-0.11857.1506-0.1544-0.14170.38430.33050.0433-0.2081-0.71010.7490.13960.9835-0.1234-0.12530.84640.03540.8238.942824.450492.5378
140.57270.24740.01992.16770.8720.98030.1362-0.422-0.44410.6202-0.164-0.31180.2617-0.00970.03460.9039-0.1187-0.24880.88550.30571.038235.8293-13.616483.1572
152.5404-0.3076-2.85363.51413.14795.31670.5368-1.39870.2491.1743-0.56240.55361.0464-1.83740.01251.8889-0.62350.38332.8752-0.01821.2634-15.71336.3675112.9705
165.66283.1875-0.08265.84920.00475.57360.3796-0.43920.03960.504-0.24270.07420.5028-0.0126-0.09270.7575-0.10350.00980.92270.0950.54872.69619.451287.1854
173.7697-2.9484-0.58173.01480.26510.78690.0128-0.1238-0.04110.5734-0.06150.1564-0.0177-0.31630.06891.097-0.28190.00850.72440.10880.7893-2.0574-15.182785.6753
186.73163.0364-1.47414.204-0.98562.7919-0.07870.3104-0.13220.23980.0964-0.0948-0.05320.0048-0.03070.75920.0115-0.07380.48870.11450.65314.7418-33.876778.0978
192.1475-2.0167-1.71232.54222.49722.60420.1479-0.7647-0.4211.80480.133-1.247-0.16460.3194-0.0942.1729-0.5716-0.16661.91580.06422.282872.78350.887568.309
209.87110.3285-1.59416.3655-0.91936.92540.0601-0.1179-0.1413-1.30590.81720.5225-0.81480.1012-0.74461.46881.0393-0.15733.1281-0.1431.2391-64.389317.16548.373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 209 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 433 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 434 through 770 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 21 through 295 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 296 through 448 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 449 through 770 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 295 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 296 through 448 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 449 through 770 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 21 through 209 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 210 through 407 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 408 through 770 )D0
13X-RAY DIFFRACTION13chain 'E' and (resid 21 through 364 )E0
14X-RAY DIFFRACTION14chain 'E' and (resid 365 through 770 )E0
15X-RAY DIFFRACTION15chain 'F' and (resid 21 through 209 )F0
16X-RAY DIFFRACTION16chain 'F' and (resid 210 through 407 )F0
17X-RAY DIFFRACTION17chain 'F' and (resid 408 through 568 )F0
18X-RAY DIFFRACTION18chain 'F' and (resid 569 through 770 )F0
19X-RAY DIFFRACTION19chain 'V' and (resid 225 through 235 )V0
20X-RAY DIFFRACTION20chain 'U' and (resid 226 through 235 )U0

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