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- PDB-5glf: Structural insights into the interaction of p97 N-terminal domain... -

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Basic information

Entry
Database: PDB / ID: 5glf
TitleStructural insights into the interaction of p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease
Components
  • Derlin-1
  • Transitional endoplasmic reticulum ATPase
KeywordsHYDROLASE/TRANSPORT PROTEIN / BETA-BARREL / ATPASE / DERLIN1 SHP BOX UBIQUITIN / PHOSPHORYLATION / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


Derlin-1-VIMP complex / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum quality control compartment / signal recognition particle binding / positive regulation of Lys63-specific deubiquitinase activity / misfolded protein binding / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair ...Derlin-1-VIMP complex / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum quality control compartment / signal recognition particle binding / positive regulation of Lys63-specific deubiquitinase activity / misfolded protein binding / 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 / 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 / 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 / response to unfolded protein / HSF1 activation / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / Protein methylation / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ATP metabolic process / : / Attachment and Entry / endoplasmic reticulum unfolded protein response / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of protein ubiquitination / proteasomal protein catabolic process / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / ADP binding / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / Translesion Synthesis by POLH / protein destabilization / 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 protein catabolic process / positive regulation of canonical Wnt signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / late endosome / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor activity / site of double-strand break / cellular response to heat / Neddylation / ATPase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / protease binding / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / early endosome / protein domain specific binding
Similarity search - Function
Derlin / Der1-like family / Vcp-like ATPase; Chain A, domain 2 - #10 / Rhomboid-like superfamily / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain ...Derlin / Der1-like family / Vcp-like ATPase; Chain A, domain 2 - #10 / Rhomboid-like superfamily / Vcp-like ATPase; Chain A, domain 2 / 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. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 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 / Derlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLim, J.J. / Lee, Y. / Yoon, S.Y. / Ly, T.T. / Kang, J.Y. / Youn, H.-S. / An, J.Y. / Lee, J.-G. / Park, K.R. / Kim, T.G. ...Lim, J.J. / Lee, Y. / Yoon, S.Y. / Ly, T.T. / Kang, J.Y. / Youn, H.-S. / An, J.Y. / Lee, J.-G. / Park, K.R. / Kim, T.G. / Yang, J.K. / Jun, Y. / Eom, S.H.
CitationJournal: FEBS Lett. / Year: 2016
Title: Structural insights into the interaction of human p97 N-terminal domain and SHP motif in Derlin-1 rhomboid pseudoprotease.
Authors: Lim, J.J. / Lee, Y. / Yoon, S.Y. / Ly, T.T. / Kang, J.Y. / Youn, H.S. / An, J.Y. / Lee, J.G. / Park, K.R. / Kim, T.G. / Yang, J.K. / Jun, Y. / Eom, S.H.
History
DepositionJul 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
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

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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: Derlin-1
C: Transitional endoplasmic reticulum ATPase
D: Derlin-1
E: Transitional endoplasmic reticulum ATPase
F: Derlin-1
G: Transitional endoplasmic reticulum ATPase
H: Derlin-1


Theoretical massNumber of molelcules
Total (without water)89,2228
Polymers89,2228
Non-polymers00
Water7,350408
1
A: Transitional endoplasmic reticulum ATPase
B: Derlin-1


Theoretical massNumber of molelcules
Total (without water)22,3062
Polymers22,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-8 kcal/mol
Surface area9790 Å2
MethodPISA
2
C: Transitional endoplasmic reticulum ATPase
D: Derlin-1


Theoretical massNumber of molelcules
Total (without water)22,3062
Polymers22,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-7 kcal/mol
Surface area9920 Å2
MethodPISA
3
E: Transitional endoplasmic reticulum ATPase
F: Derlin-1


Theoretical massNumber of molelcules
Total (without water)22,3062
Polymers22,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area9530 Å2
MethodPISA
4
G: Transitional endoplasmic reticulum ATPase
H: Derlin-1


Theoretical massNumber of molelcules
Total (without water)22,3062
Polymers22,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.802, 74.402, 222.114
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
21C
12A
22E
13A
23G
14C
24E
15C
25G
16E
26G

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROARGARGAA23 - 1918 - 176
21PROPROARGARGCC23 - 1918 - 176
12ASNASNARGARGAA24 - 1919 - 176
22ASNASNARGARGEE24 - 1919 - 176
13PROPROILEILEAA23 - 1898 - 174
23PROPROILEILEGG23 - 1898 - 174
14ASNASNARGARGCC24 - 1919 - 176
24ASNASNARGARGEE24 - 1919 - 176
15PROPROILEILECC23 - 1898 - 174
25PROPROILEILEGG23 - 1898 - 174
16ASNASNILEILEEE24 - 1899 - 174
26ASNASNILEILEGG24 - 1899 - 174

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 20859.961 Da / Num. of mol.: 4 / Fragment: P97 N-TERMINAL DOMAIN (UNP RESIDUES 21-199)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli (E. coli) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein/peptide
Derlin-1 / / Degradation in endoplasmic reticulum protein 1 / DERtrin-1 / Der1-like protein 1


Mass: 1445.566 Da / Num. of mol.: 4 / Fragment: SHP BOX (UNP RESIDUES 239-250) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BUN8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.03 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, BIS-TRIS PH 6.5, 0.2M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 34582 / % possible obs: 98.9 % / Redundancy: 10 % / Net I/σ(I): 9.1
Reflection shellResolution: 2.25→2.29 Å

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0103refinement
HKL-2000data reduction
MOLREPdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ7

3qq7


Resolution: 2.25→42.97 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.739 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.233 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1716 5 %RANDOM
Rwork0.189 ---
obs0.191 32415 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.25→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5763 0 0 408 6171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195862
X-RAY DIFFRACTIONr_bond_other_d0.0090.025800
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9757906
X-RAY DIFFRACTIONr_angle_other_deg1.797313333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4355713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69723.262282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.357151075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5521565
X-RAY DIFFRACTIONr_chiral_restr0.1040.2889
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216489
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021300
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9253.4262876
X-RAY DIFFRACTIONr_mcbond_other2.9243.4252875
X-RAY DIFFRACTIONr_mcangle_it4.4435.1173581
X-RAY DIFFRACTIONr_mcangle_other4.4445.1183582
X-RAY DIFFRACTIONr_scbond_it3.863.9512986
X-RAY DIFFRACTIONr_scbond_other3.8593.9522987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0325.7244326
X-RAY DIFFRACTIONr_long_range_B_refined8.52327.6876578
X-RAY DIFFRACTIONr_long_range_B_other8.46227.5526487
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A207800.13
12C207800.13
21A209300.12
22E209300.12
31A206320.12
32G206320.12
41C206060.13
42E206060.13
51C203760.14
52G203760.14
61E206360.12
62G206360.12
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 89 -
Rwork0.216 2129 -
obs--86.4 %

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