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- PDB-2fmx: An open conformation of switch I revealed by Sar1-GDP crystal str... -

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Basic information

Entry
Database: PDB / ID: 2fmx
TitleAn open conformation of switch I revealed by Sar1-GDP crystal structure at low Mg(2+)
ComponentsGTP-binding protein SAR1b
KeywordsPROTEIN TRANSPORT / Sar1 / COP II assembly / dimerization
Function / homology
Function and homology information


lipid export from cell / regulation of lipid transport / regulation of COPII vesicle coating / COPII-coated vesicle cargo loading / COPII vesicle coat / COPII vesicle coating / positive regulation of protein exit from endoplasmic reticulum / lipoprotein transport / Golgi cisterna membrane / lipid homeostasis ...lipid export from cell / regulation of lipid transport / regulation of COPII vesicle coating / COPII-coated vesicle cargo loading / COPII vesicle coat / COPII vesicle coating / positive regulation of protein exit from endoplasmic reticulum / lipoprotein transport / Golgi cisterna membrane / lipid homeostasis / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / small monomeric GTPase / intracellular protein transport / G protein activity / lysosomal membrane / endoplasmic reticulum membrane / GTP binding / metal ion binding / cytosol
Similarity search - Function
small GTPase SAR1 family profile. / Small GTPase superfamily, SAR1-type / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...small GTPase SAR1 family profile. / Small GTPase superfamily, SAR1-type / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Small COPII coat GTPase SAR1B
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsRao, Y. / Bian, C. / Yuan, C. / Li, Y. / Huang, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: An open conformation of switch I revealed by Sar1-GDP crystal structure at low Mg(2+)
Authors: Rao, Y. / Bian, C. / Yuan, C. / Li, Y. / Chen, L. / Ye, X. / Huang, Z. / Huang, M.
History
DepositionJan 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_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.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_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

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Assembly

Deposited unit
A: GTP-binding protein SAR1b
B: GTP-binding protein SAR1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2257
Polymers44,1232
Non-polymers1,1035
Water3,585199
1
A: GTP-binding protein SAR1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6013
Polymers22,0611
Non-polymers5392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein SAR1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6254
Polymers22,0611
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.825, 61.993, 71.126
Angle α, β, γ (deg.)90.00, 107.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding protein SAR1b / Sar1 / GTBPB


Mass: 22061.332 Da / Num. of mol.: 2 / Fragment: residues 10-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Plasmid: PET11d / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QVY3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.6
Details: 28%(w/v)Polyethylene Glycol-4000, 100mM sodium acetate, 0.2M ammonium sulfate, pH 5.6, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ENRAF-NONIUS GX-21 / Detector: CCD / Date: Aug 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→39.07 Å / Num. all: 35092 / Num. obs: 35092 / % possible obs: 88.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2 / % possible all: 63.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→39.07 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1269885.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2086 5.9 %RANDOM
Rwork0.224 ---
obs0.224 35076 88.6 %-
all-35076 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.3898 Å2 / ksol: 0.371957 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.68 Å20 Å2-1.46 Å2
2---4.46 Å20 Å2
3----3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.82→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 67 199 3044
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.542
X-RAY DIFFRACTIONc_scangle_it2.362.5
LS refinement shellResolution: 1.82→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 201 6.5 %
Rwork0.273 2884 -
obs--45.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION29sar1wt_xplor_par.txt
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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