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- PDB-1m2v: Crystal Structure of the yeast Sec23/24 heterodimer -

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Basic information

Entry
Database: PDB / ID: 1m2v
TitleCrystal Structure of the yeast Sec23/24 heterodimer
Components
  • protein transport protein SEC23
  • protein transport protein SEC24
KeywordsPROTEIN TRANSPORT / zinc-finger / beta barrel / vWA domain / gelsolin domain
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 / COPII-mediated vesicle transport / COPII-coated vesicle cargo loading / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coat / signal sequence binding / fungal-type vacuole membrane ...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 / COPII-mediated vesicle transport / COPII-coated vesicle cargo loading / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coat / signal sequence binding / fungal-type vacuole membrane / reticulophagy / endoplasmic reticulum exit site / GTPase activator activity / SNARE binding / macroautophagy / intracellular protein transport / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / zinc ion binding
Similarity search - Function
Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Sec23, C-terminal / Protein transport protein Sec23 / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / : / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain ...Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Sec23, C-terminal / Protein transport protein Sec23 / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / : / 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 / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor, type A domain / von Willebrand factor A-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / Roll / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein transport protein SEC23 / Protein transport protein SEC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 25, 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: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Assembly

Deposited unit
A: protein transport protein SEC23
B: protein transport protein SEC24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,3274
Polymers189,1962
Non-polymers1312
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.309, 126.371, 180.200
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

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


Mass: 85463.242 Da / Num. of mol.: 1
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 protein transport protein SEC24 / Sec24 / Sec24p / SEC24 protein / Abnormal nuclear morphology 1 Sec24 COPII-coat protein


Mass: 103733.250 Da / Num. of mol.: 1
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: P40482
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0 M ammonium formate, 18 mM dithiothreitol, 10 % (w/v) xylitol, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP at 273K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
135 mg/mlprotein1drop
215 %(w/v)xylitol1drop
31.0 Mammonium formate1drop
418 mMdithiothreitol1drop
50.1 MHEPES1droppH7.5
61.9 Mammonium formate1reservoir
70.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.05 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. all: 54236 / Num. obs: 49463 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.75→2.92 Å
Reflection
*PLUS
Num. measured all: 190671 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 63.1 % / Rmerge(I) obs: 0.252

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Sec23 from PDB ENTRY 1M2O

1m2o


Resolution: 2.75→19.96 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2388 5.1 %RANDOM
Rwork0.21 ---
obs0.21 49495 91.2 %-
all-54236 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.2334 Å2 / ksol: 0.374578 e/Å3
Displacement parametersBiso mean: 52.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.87 Å20 Å20 Å2
2--7.31 Å20 Å2
3----13.19 Å2
Refine analyzeLuzzati coordinate error free: 0.41 Å / Luzzati sigma a free: 0.62 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11506 0 2 69 11577
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 326 5.4 %
Rwork0.332 5694 -
obs--67.5 %
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 DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor obs: 0.21 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor Rfree: 0.397 / Rfactor Rwork: 0.332

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