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- PDB-1m2o: Crystal Structure of the Sec23-Sar1 complex -

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Basic information

Entry
Database: PDB / ID: 1m2o
TitleCrystal Structure of the Sec23-Sar1 complex
Components
  • GTP-binding protein SAR1
  • protein transport protein SEC23
KeywordsPROTEIN TRANSPORT/SIGNALING PROTEIN / zinc-finger / beta barrel / vWA domain / gelsolin domain / PROTEIN TRANSPORT-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / regulation of COPII vesicle coating / positive regulation of ER to Golgi vesicle-mediated transport / nuclear envelope organization / COPII-mediated vesicle transport / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-coated vesicle cargo loading / positive regulation of protein exit from endoplasmic reticulum / vesicle organization ...Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / regulation of COPII vesicle coating / positive regulation of ER to Golgi vesicle-mediated transport / nuclear envelope organization / COPII-mediated vesicle transport / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-coated vesicle cargo loading / positive regulation of protein exit from endoplasmic reticulum / vesicle organization / COPII vesicle coat / membrane organization / mitochondrial fission / reticulophagy / mitochondrial membrane organization / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / GTPase activator activity / macroautophagy / intracellular protein transport / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum / mitochondrion / zinc ion binding
Similarity search - Function
Small GTPase SAR1 domain profile. / Small GTPase superfamily, SAR1-type / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Sec23, C-terminal / Protein transport protein Sec23 / Zn-finger domain of Sec23/24 / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain ...Small GTPase SAR1 domain profile. / Small GTPase superfamily, SAR1-type / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Sec23, C-terminal / Protein transport protein Sec23 / Zn-finger domain of Sec23/24 / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Sec23/Sec24 beta-sandwich domain / Gelsolin-like domain superfamily / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ADF-H/Gelsolin-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / von Willebrand factor, type A domain / von Willebrand factor A-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / Small GTP-binding protein domain / Roll / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Protein transport protein SEC23 / Small COPII coat GTPase SAR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsBi, X. / Corpina, R.A. / Goldberg, J.
CitationJournal: Nature / Year: 2002
Title: Structure of the Sec23/24-Sar1 pre-budding complex of the COPII vesicle coat
Authors: Bi, X. / Corpina, R.A. / Goldberg, J.
History
DepositionJun 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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_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_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: protein transport protein SEC23
B: GTP-binding protein SAR1
C: protein transport protein SEC23
D: GTP-binding protein SAR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,09510
Polymers213,8724
Non-polymers1,2246
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: protein transport protein SEC23
D: GTP-binding protein SAR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5485
Polymers106,9362
Non-polymers6123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-28 kcal/mol
Surface area35970 Å2
MethodPISA, PQS
3
A: protein transport protein SEC23
B: GTP-binding protein SAR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5485
Polymers106,9362
Non-polymers6123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-24 kcal/mol
Surface area36270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.196, 151.158, 271.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein protein transport protein SEC23 / Sec23 / Sec23p / cytoplasmic GTPase-activating protein / Sec23 COPII-coat protein


Mass: 85463.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Sec23 / Production host: Escherichia coli (E. coli) / References: UniProt: P15303
#2: Protein GTP-binding protein SAR1 / Sar1p / a GTP-binding protein / GTP binding protein Sar1p / Sar1 G-protein


Mass: 21472.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Sar1 / Production host: Escherichia coli (E. coli) / References: UniProt: P20606

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Non-polymers , 4 types, 177 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 270 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% (w/v) PEG 1500, 10% (w/v) isopropanol, 0.2 M ammonium acetate, 50 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 270K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
144 mg/mlprotein1drop
212 %(w/v)PEG15001reservoir
310 %(v/v)isopropanol1reservoir
40.2 Mammonium acetate1reservoir
550 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1 Å
DetectorType: KODAK / Detector: IMAGE PLATE / Date: Nov 5, 2001
RadiationMonochromator: CHESS F-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 68753 / Num. obs: 63872 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.046
Reflection shellResolution: 2.5→2.66 Å
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 289977 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 79.9 % / Rmerge(I) obs: 0.237

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→23.85 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 3007 5.1 %RANDOM
Rwork0.238 ---
all0.238 68753 --
obs0.238 62523 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.6345 Å2 / ksol: 0.312224 e/Å3
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1-23.43 Å20 Å20 Å2
2---11.54 Å20 Å2
3----11.89 Å2
Refine analyzeLuzzati coordinate error free: 0.45 Å / Luzzati sigma a free: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.5→23.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13884 0 68 171 14123
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 397 5.3 %
Rwork0.282 7952 -
obs--79.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GMPPNP.PARAMGMPPNP.TOPOL
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.238 / Rfactor obs: 0.238 / Rfactor Rfree: 0.295 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Rfactor Rfree: 0.368 / Rfactor Rwork: 0.282

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