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- PDB-1cr5: N-TERMINAL DOMAIN OF SEC18P -

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Basic information

Entry
Database: PDB / ID: 1cr5
TitleN-TERMINAL DOMAIN OF SEC18P
ComponentsSEC18P (RESIDUES 22 - 210)
KeywordsENDOCYTOSIS/EXOCYTOSIS / DOUBLE-PSI BETA BARREL / VESICLE FUSION / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


inter-Golgi cisterna vesicle-mediated transport / Retrograde transport at the Trans-Golgi-Network / vesicle fusion with Golgi apparatus / Intra-Golgi traffic / vacuole fusion, non-autophagic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / SNARE complex disassembly / phosphatidic acid binding ...inter-Golgi cisterna vesicle-mediated transport / Retrograde transport at the Trans-Golgi-Network / vesicle fusion with Golgi apparatus / Intra-Golgi traffic / vacuole fusion, non-autophagic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / SNARE complex disassembly / phosphatidic acid binding / intra-Golgi vesicle-mediated transport / mating projection tip / Golgi to plasma membrane protein transport / Golgi stack / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / SNARE binding / macroautophagy / Golgi apparatus / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Vesicle-fusing ATPase / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / 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 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Vesicle-fusing ATPase / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / 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
1-ETHYL-PYRROLIDINE-2,5-DIONE / Vesicular-fusion protein SEC18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBabor, S.M. / Fass, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of the Sec18p N-terminal domain.
Authors: Babor, S.M. / Fass, D.
History
DepositionAug 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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_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: SEC18P (RESIDUES 22 - 210)
B: SEC18P (RESIDUES 22 - 210)
C: SEC18P (RESIDUES 22 - 210)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7359
Polymers63,9723
Non-polymers7636
Water4,864270
1
A: SEC18P (RESIDUES 22 - 210)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5783
Polymers21,3241
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SEC18P (RESIDUES 22 - 210)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5783
Polymers21,3241
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SEC18P (RESIDUES 22 - 210)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5783
Polymers21,3241
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.710, 32.140, 94.850
Angle α, β, γ (deg.)90.00, 118.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SEC18P (RESIDUES 22 - 210)


Mass: 21323.959 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / References: UniProt: P18759
#2: Chemical
ChemComp-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


Mass: 127.141 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H9NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 8000, sodium phosphate, dimethyl sulfoxide, ATP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMsodium phosphate1drop
210 mg/mlprotein1drop
350 mMsodium phosphate1reservoir
45-10 %DMSO1reservoir
55 %PEG80001reservoir
65 mMATP1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 22632 / Num. obs: 22366 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Redundancy: 4 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.115 / Num. unique all: 2200 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 176811 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→20 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1547 -random
Rwork0.23 ---
all-22661 --
obs-22187 97.9 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 0 54 270 4555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.344
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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