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- PDB-3tiw: Crystal structure of p97N in complex with the C-terminus of gp78 -

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Basic information

Entry
Database: PDB / ID: 3tiw
TitleCrystal structure of p97N in complex with the C-terminus of gp78
Components
  • E3 ubiquitin-protein ligase AMFR
  • Transitional endoplasmic reticulum ATPase
KeywordsPROTEIN TRANSPORT/Ligase / beta-barrel alpha-helix / transport protein ATPase ubiquitin ligase / ubiquitin / Phosphorylation / cytoplasm endoplasmic reticulum / PROTEIN TRANSPORT-Ligase complex
Function / homology
Function and homology information


regulation of SREBP signaling pathway / positive regulation of plant-type hypersensitive response / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control ...regulation of SREBP signaling pathway / positive regulation of plant-type hypersensitive response / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / 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 / ubiquitin-modified protein reader activity / ubiquitin-ubiquitin ligase activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / non-canonical NF-kappaB signal transduction / ubiquitin-like protein ligase binding / MHC class I protein binding / RHOH GTPase cycle / autophagosome maturation / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / protein autoubiquitination / protein K48-linked ubiquitination / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ERAD pathway / ATP metabolic process / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / ER Quality Control Compartment (ERQC) / Attachment and Entry / lipid droplet / viral genome replication / proteasome complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / Hh mutants are degraded by ERAD / macroautophagy / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / negative regulation of canonical Wnt signaling pathway / ABC-family proteins mediated transport / ADP binding / Wnt signaling pathway / autophagy / cytoplasmic stress granule / Aggrephagy / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / ubiquitin protein ligase activity / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / protein-macromolecule adaptor activity / Neddylation / signaling receptor activity / site of double-strand break / cellular response to heat / protein-folding chaperone binding / growth cone / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process
Similarity search - Function
E3 ubiquitin-protein ligase AMFR, Ube2g2-binding region / E3 gp78 Ube2g2-binding region (G2BR) / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Ring finger domain / Barwin-like endoglucanases - #20 ...E3 ubiquitin-protein ligase AMFR, Ube2g2-binding region / E3 gp78 Ube2g2-binding region (G2BR) / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Ring finger domain / Barwin-like endoglucanases - #20 / 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. / Ring finger / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transitional endoplasmic reticulum ATPase / E3 ubiquitin-protein ligase AMFR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.802 Å
AuthorsHaenzelmann, P. / Schindelin, H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Structural and Functional Basis of the p97/Valosin-containing Protein (VCP)-interacting Motif (VIM): MUTUALLY EXCLUSIVE BINDING OF COFACTORS TO THE N-TERMINAL DOMAIN OF p97.
Authors: Hanzelmann, P. / Schindelin, H.
History
DepositionAug 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: 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 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
C: E3 ubiquitin-protein ligase AMFR
B: Transitional endoplasmic reticulum ATPase
D: E3 ubiquitin-protein ligase AMFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8268
Polymers46,6844
Non-polymers1424
Water6,864381
1
A: Transitional endoplasmic reticulum ATPase
C: E3 ubiquitin-protein ligase AMFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4134
Polymers23,3422
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-21 kcal/mol
Surface area9960 Å2
MethodPISA
2
B: Transitional endoplasmic reticulum ATPase
D: E3 ubiquitin-protein ligase AMFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4134
Polymers23,3422
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-21 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.240, 70.240, 74.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROASPASPchain A and (resseq 23:121 or resseq 128:185 )AA23 - 12123 - 121
121GLYGLYGLUGLUchain A and (resseq 23:121 or resseq 128:185 )AA128 - 185128 - 185
211PROPROASPASPchain B and (resseq 23:121 or resseq 128:185 )BC23 - 12123 - 121
221GLYGLYGLUGLUchain B and (resseq 23:121 or resseq 128:185 )BC128 - 185128 - 185
112VALVALLYSLYSchain C and (resseq 622:639 )CB622 - 6391 - 18
212VALVALLYSLYSchain D and (resseq 622:639 )DD622 - 6391 - 18

NCS ensembles :
ID
1
2

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Components

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


Mass: 21068.277 Da / Num. of mol.: 2 / Fragment: unp residues 1-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Plasmid: pProEx_HTa / Production host: Escherichia coli (E. coli) / References: UniProt: P55072
#2: Protein/peptide E3 ubiquitin-protein ligase AMFR / Autocrine motility factor receptor / isoform 2 / AMF receptor / isoform 2 / RING finger protein 45 / gp78


Mass: 2273.750 Da / Num. of mol.: 2 / Fragment: unp residues 622-640 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18-22% (w/v) polyethylene glycol 3000, 0.2 M NaCl and 100 mM Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.292
ReflectionResolution: 1.802→60.829 Å / Num. all: 38133 / Num. obs: 38133 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.93.80.4921.62105456020.492100
1.9-2.023.80.32.52007652670.3100
2.02-2.153.80.1983.71886049220.198100
2.15-2.333.80.1474.81772946170.147100
2.33-2.553.90.13251626442180.132100
2.55-2.853.90.10761492738540.107100
2.85-3.293.90.0986.31305733670.098100
3.29-4.033.90.0976.31113628650.097100
4.03-5.73.90.0876.8867222220.087100
5.7-35.123.90.0716.8461911990.07199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASERphasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1S3S

1s3s


Resolution: 1.802→35.12 Å / Occupancy max: 1 / Occupancy min: 0.33 / σ(F): 0 / Phase error: 25.89 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1705 1903 4.99 %random
Rwork0.1468 ---
all0.1482 38107 --
obs0.1482 38107 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.221 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 163.48 Å2 / Biso mean: 33.072 Å2 / Biso min: 11.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.761 Å20 Å20 Å2
2---1.761 Å2-0 Å2
3---3.5219 Å2
Refinement stepCycle: LAST / Resolution: 1.802→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 4 381 3244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062948
X-RAY DIFFRACTIONf_angle_d1.0573984
X-RAY DIFFRACTIONf_chiral_restr0.067459
X-RAY DIFFRACTIONf_plane_restr0.004521
X-RAY DIFFRACTIONf_dihedral_angle_d13.741182
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1254X-RAY DIFFRACTIONPOSITIONAL0.906
12B1254X-RAY DIFFRACTIONPOSITIONAL0.906
21C140X-RAY DIFFRACTIONPOSITIONAL1.042
22D140X-RAY DIFFRACTIONPOSITIONAL1.042
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8024-1.85110.35281590.33342763292295
1.8511-1.90550.28151370.27952790292795
1.9055-1.9670.27031510.23442784293595
1.967-2.03730.23031080.22352807291596
2.0373-2.11880.20221380.19132789292795
2.1188-2.21520.1981300.18022806293696
2.2152-2.33180.19191480.17652824297295
2.3318-2.47780.21031390.17352748288795
2.4778-2.66880.16761450.16632789293495
2.6688-2.93690.18511560.15012791294795
2.9369-3.36080.15481590.12112755291495
3.3608-4.230.13371740.09322756293094
4.23-23.07770.12931590.0982781294095
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)
11.9917-0.87940.03351.2205-0.09780.14030.0473-0.0790.07930.0106-0.0211-0.092-0.02130.02-0.01410.11480.00180.00180.1006-0.00250.123222.7204-16.7094-7.7164
21.5487-0.50280.03910.5546-0.21110.63930.0666-0.15540.8257-0.0337-0.0438-0.0672-0.17610.0648-0.02940.1575-0.01490.060.1071-0.07270.401715.90382.771-4.7897
31.9833-1.65740.01411.63080.51840.7007-0.031-0.1833-0.53070.04770.04270.28020.14580.0009-0.01210.08150.02980.03220.13150.0590.28222.6543-15.433430.0395
41.1483-0.8702-0.08891.52880.12370.61650.0176-0.1490.023-0.1537-0.0550.05590.05540.08140.02210.10480.00630.01320.13880.0010.175514.82733.93931.1546
50.5507-0.12710.44880.2479-0.01970.36730.23080.28660.2795-0.0251-0.28670.06110.05610.09960.00090.14120.04380.02230.21820.06320.173115.0534-7.6333-20.7375
61.37440.0460.57140.9231-0.23620.34470.35060.5646-0.2228-0.1648-0.22490.35250.1349-0.0631-0.12880.17670.0779-0.03350.2103-0.02870.265514.3764-8.460416.9439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 22:108)A22 - 108
2X-RAY DIFFRACTION2(chain A and resid 109:186)A109 - 186
3X-RAY DIFFRACTION3(chain B and resid 23:108)B23 - 108
4X-RAY DIFFRACTION4(chain B and resid 109:187)B109 - 187
5X-RAY DIFFRACTION5(chain C and resid 622:639)C622 - 639
6X-RAY DIFFRACTION6(chain D and resid 622:640)D622 - 640

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