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- PDB-1d2n: D2 DOMAIN OF N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1d2n
TitleD2 DOMAIN OF N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN
ComponentsN-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN
KeywordsHEXAMERIZATION DOMAIN / ATPASE / TRANSPORT
Function / homology
Function and homology information


SNARE complex disassembly / ATP-dependent protein disaggregase activity / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding / PDZ domain binding / intracellular protein transport / potassium ion transport ...SNARE complex disassembly / ATP-dependent protein disaggregase activity / vesicle-fusing ATPase / syntaxin-1 binding / positive regulation of receptor recycling / ionotropic glutamate receptor binding / SNARE binding / PDZ domain binding / intracellular protein transport / potassium ion transport / positive regulation of protein catabolic process / midbody / protein-containing complex binding / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Vesicle-fusing ATPase / Helicase, Ruva Protein; domain 3 - #60 / 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 ...Vesicle-fusing ATPase / Helicase, Ruva Protein; domain 3 - #60 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Vesicle-fusing ATPase
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.75 Å
AuthorsLenzen, C.U. / Steinmann, D. / Whiteheart, S.W. / Weis, W.I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein.
Authors: Lenzen, C.U. / Steinmann, D. / Whiteheart, S.W. / Weis, W.I.
History
DepositionJun 30, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_conn.ptnr2_label_seq_id / _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: N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1604
Polymers30,5381
Non-polymers6233
Water4,882271
1
A: N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)186,96124
Polymers183,2266
Non-polymers3,73618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area23830 Å2
ΔGint-131 kcal/mol
Surface area60780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.330, 116.330, 40.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

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Components

#1: Protein N-ETHYLMALEIMIDE-SENSITIVE FUSION PROTEIN


Mass: 30537.607 Da / Num. of mol.: 1 / Fragment: D2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Cellular location: CYTOPLASM / Organ: OVARY / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P18708
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.57 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / pH: 8
Details: 3-8% PEG 3350, 300 MM KCL, 100 MM TRIS-HCL, PH 8.0, 5 MM MGCL2, 5 MM GDCL3, 2 MM DTT, 2 MM AMP-PNP, temperature 293K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
23-8 %PEG33501reservoir
3100 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: GRAPHITE MONOCHROMATOR, 0.3 MM COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 31212 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052
Reflection shellResolution: 1.75→1.83 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Rsym value: 0.26 / % possible all: 91.6
Reflection shell
*PLUS
% possible obs: 91.6 % / Num. unique obs: 3600 / Rmerge(I) obs: 0.26

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Processing

Software
NameVersionClassification
DMmodel building
MLPHAREphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.75→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2984 10 %RANDOM
Rwork0.199 ---
obs0.199 29919 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.5 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å2-1.1 Å20 Å2
2---2.8 Å20 Å2
3---5.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 38 271 2238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_scangle_it3.732.5
LS refinement shellResolution: 1.75→1.83 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.276 312 10.1 %
Rwork0.255 2762 -
obs--78.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-ATP_REP.PARAMATP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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