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- PDB-4rv0: Crystal structure of TN complex -

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Basic information

Entry
Database: PDB / ID: 4rv0
TitleCrystal structure of TN complex
Components
  • Nuclear protein localization protein 4 homolog
  • Transitional endoplasmic reticulum ATPase TER94
KeywordsPROTEIN BINDING / TRANSPORT PROTEIN / Ter94/p97 / Npl4 / AAA ATPase
Function / homology
Function and homology information


RHOH GTPase cycle / HSF1 activation / K11-linked polyubiquitin modification-dependent protein binding / lysosomal membrane organization / larval midgut cell programmed cell death / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Translesion Synthesis by POLH / ABC-family proteins mediated transport / KEAP1-NFE2L2 pathway ...RHOH GTPase cycle / HSF1 activation / K11-linked polyubiquitin modification-dependent protein binding / lysosomal membrane organization / larval midgut cell programmed cell death / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Translesion Synthesis by POLH / ABC-family proteins mediated transport / KEAP1-NFE2L2 pathway / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / Hedgehog ligand biogenesis / fusome / Neddylation / regulation of pole plasm oskar mRNA localization / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / pole cell formation / endoplasmic reticulum membrane fusion / Neutrophil degranulation / autophagosome-lysosome fusion / DNA clamp loader activity / endoplasmic reticulum organization / mitotic spindle disassembly / P granule / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / retrograde protein transport, ER to cytosol / lysosome organization / oogenesis / muscle cell cellular homeostasis / dendrite morphogenesis / Golgi organization / autolysosome / polyubiquitin modification-dependent protein binding / autophagosome maturation / negative regulation of hippo signaling / regulation of neuron apoptotic process / protein sequestering activity / ubiquitin binding / negative regulation of smoothened signaling pathway / negative regulation of canonical Wnt signaling pathway / cellular response to virus / microtubule cytoskeleton organization / positive regulation of neuron apoptotic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of viral entry into host cell / lysosomal membrane / ubiquitin protein ligase binding / ATP hydrolysis activity / proteolysis / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Vps4 oligomerisation, C-terminal ...Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain / Zinc 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 / : / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / MPN domain / MPN domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin-like domain superfamily / 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 TER94 / Nuclear protein localization protein 4 homolog / Isoform B of Nuclear protein localization protein 4 homolog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.998 Å
AuthorsHao, Q. / Jiao, S. / Shi, Z.B. / Zhou, Z.C.
CitationJournal: To be Published
Title: Crystal structure of TN complex
Authors: Hao, Q. / Jiao, S. / Shi, Z.B. / Zhou, Z.C.
History
DepositionNov 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase TER94
B: Nuclear protein localization protein 4 homolog
C: Transitional endoplasmic reticulum ATPase TER94
D: Nuclear protein localization protein 4 homolog
E: Transitional endoplasmic reticulum ATPase TER94
F: Nuclear protein localization protein 4 homolog
G: Transitional endoplasmic reticulum ATPase TER94
H: Nuclear protein localization protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,00415
Polymers115,3328
Non-polymers6727
Water18,8441046
1
A: Transitional endoplasmic reticulum ATPase TER94
B: Nuclear protein localization protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0254
Polymers28,8332
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Transitional endoplasmic reticulum ATPase TER94
D: Nuclear protein localization protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0254
Polymers28,8332
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Transitional endoplasmic reticulum ATPase TER94
F: Nuclear protein localization protein 4 homolog


Theoretical massNumber of molelcules
Total (without water)28,8332
Polymers28,8332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Transitional endoplasmic reticulum ATPase TER94
H: Nuclear protein localization protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1215
Polymers28,8332
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.146, 83.141, 162.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Transitional endoplasmic reticulum ATPase TER94 / Valosin-containing protein homolog


Mass: 19617.834 Da / Num. of mol.: 4 / Fragment: N domain, UNP residues 20-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG2331, TER94, VCP / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7KN62, vesicle-fusing ATPase
#2: Protein
Nuclear protein localization protein 4 homolog


Mass: 9215.136 Da / Num. of mol.: 4 / Fragment: UBD domain, UNP residues 1-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG4673, Npl4 / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VBP9-2, UniProt: Q9VBP9*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1046 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsENTITY 2 IS BASED ON ISOFORM 2 OF DATABASE NPL4_DROME (Q9VBP9-2)

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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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 23% w/v polyethylene glycol 3350, 0.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9791 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.998→50 Å / Num. all: 74276 / Num. obs: 74127 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Biso Wilson estimate: 19.67 Å2 / Rmerge(I) obs: 0.16
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.18 / Num. unique all: 3503 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.998→45.384 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 3725 5.04 %RANDOM
Rwork0.2082 ---
all0.2104 74272 --
obs0.2104 73967 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.8 Å2
Refinement stepCycle: LAST / Resolution: 1.998→45.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7272 0 35 1046 8353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087462
X-RAY DIFFRACTIONf_angle_d1.28110069
X-RAY DIFFRACTIONf_dihedral_angle_d14.292879
X-RAY DIFFRACTIONf_chiral_restr0.081150
X-RAY DIFFRACTIONf_plane_restr0.0061301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9983-2.02360.3281360.2794236692
2.0236-2.05020.27281250.2425257399
2.0502-2.07830.28941380.23652591100
2.0783-2.1080.2731340.21232563100
2.108-2.13940.27891300.22372600100
2.1394-2.17290.28191470.23332569100
2.1729-2.20850.3121360.25842548100
2.2085-2.24660.35871140.31232611100
2.2466-2.28740.38741400.28082579100
2.2874-2.33140.28331370.26052570100
2.3314-2.3790.29291440.20562603100
2.379-2.43070.27611410.20332595100
2.4307-2.48730.26221340.20172568100
2.4873-2.54950.26781340.19822595100
2.5495-2.61840.21971360.19972622100
2.6184-2.69540.30391470.19952600100
2.6954-2.78240.24531470.20812573100
2.7824-2.88190.26411320.20262625100
2.8819-2.99720.22881540.1972572100
2.9972-3.13360.25761160.20252629100
3.1336-3.29880.22431150.19462654100
3.2988-3.50540.21561440.19372628100
3.5054-3.77590.20581270.18222647100
3.7759-4.15560.22191520.17682641100
4.1556-4.75640.18181690.15912628100
4.7564-5.99040.24251420.19232696100
5.9904-45.39520.28531540.237279699

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