[English] 日本語
Yorodumi
- PDB-4h5i: Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h5i
TitleCrystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)
ComponentsGuanine nucleotide-exchange factor SEC12
KeywordsPROTEIN TRANSPORT / COPII vesicle budding / potassium binding site / beta propeller
Function / homology
Function and homology information


regulation of COPII vesicle coating / COPII-mediated vesicle transport / protein secretion / vesicle-mediated transport / GTPase activator activity / guanyl-nucleotide exchange factor activity / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
Guanine nucleotide-exchange factor Sec12-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / Guanine nucleotide-exchange factor SEC12
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsMcMahon, C. / Jeffrey, P.D. / Hughson, F.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The structure of sec12 implicates potassium ion coordination in sar1 activation.
Authors: McMahon, C. / Studer, S.M. / Clendinen, C. / Dann, G.P. / Jeffrey, P.D. / Hughson, F.M.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanine nucleotide-exchange factor SEC12
B: Guanine nucleotide-exchange factor SEC12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6166
Polymers80,4592
Non-polymers1564
Water7,710428
1
A: Guanine nucleotide-exchange factor SEC12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3083
Polymers40,2301
Non-polymers782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Guanine nucleotide-exchange factor SEC12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3083
Polymers40,2301
Non-polymers782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.400, 53.474, 61.976
Angle α, β, γ (deg.)81.680, 73.370, 87.580
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Guanine nucleotide-exchange factor SEC12 / Protein transport protein SEC12


Mass: 40229.582 Da / Num. of mol.: 2 / Fragment: UNP residues 1-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC12, SED2, YNR026C, N3244 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11655
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 100 mM Tris, pH 8.0, 400 mM potassium chloride, 22% w/v PEG3350, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 132685 / % possible obs: 93.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Χ2: 1.379 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.35-1.373.50.6156810.869179.8
1.37-1.43.70.53465150.715191.9
1.4-1.433.80.46665210.719192.2
1.43-1.453.80.42265220.833192.4
1.45-1.493.80.35966030.884192.6
1.49-1.523.80.365900.92193.1
1.52-1.563.80.23566190.946193.4
1.56-1.63.80.19166610.87194
1.6-1.653.90.16866530.903194.2
1.65-1.73.90.14366930.929194.5
1.7-1.763.90.11967391.07195
1.76-1.833.90.09567801.108195.1
1.83-1.923.90.09267261.583195.4
1.92-2.023.90.06967751.613195.9
2.02-2.143.80.06268361.844196
2.14-2.313.80.05568422.025196.3
2.31-2.543.80.04969052.016197.3
2.54-2.913.70.04568672.354197.6
2.91-3.663.60.03869222.619197.4
3.66-503.70.03662352.735188.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_1144refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→42.359 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.13 / σ(F): 1.98 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 6617 5.01 %
Rwork0.1786 --
obs0.1795 132033 94.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.11 Å2 / Biso mean: 15.019 Å2 / Biso min: 5 Å2
Refinement stepCycle: LAST / Resolution: 1.36→42.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5249 0 4 428 5681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115341
X-RAY DIFFRACTIONf_angle_d1.2487223
X-RAY DIFFRACTIONf_chiral_restr0.088865
X-RAY DIFFRACTIONf_plane_restr0.005911
X-RAY DIFFRACTIONf_dihedral_angle_d12.1321953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.36-1.37550.28871780.25343686386482
1.3755-1.39170.25642260.24764046427292
1.3917-1.40860.26412100.22764110432091
1.4086-1.42650.24392160.22124045426193
1.4265-1.44520.24562110.21124118432992
1.4452-1.4650.21572310.21174059429093
1.465-1.4860.24752340.20894125435993
1.486-1.50810.22342250.19714067429293
1.5081-1.53170.20382040.19654091429593
1.5317-1.55680.22432120.18414159437194
1.5568-1.58370.21372300.18214138436894
1.5837-1.61250.21592150.18274200441594
1.6125-1.64350.20222210.1754153437494
1.6435-1.6770.20132330.17394187442094
1.677-1.71350.20862250.17444152437795
1.7135-1.75340.20472270.17324184441195
1.7534-1.79720.18372090.17274219442895
1.7972-1.84580.212460.17224231447795
1.8458-1.90010.19012010.17524246444796
1.9001-1.96140.20392290.17024215444496
1.9614-2.03150.17892110.16694299451096
2.0315-2.11290.1952000.16944249444996
2.1129-2.2090.17982080.16654312452097
2.209-2.32550.19572360.18264257449397
2.3255-2.47120.20412380.1874280451897
2.4712-2.66190.20192430.19424336457997
2.6619-2.92980.21872220.18994293451598
2.9298-3.35360.18792160.17444362457898
3.3536-4.22450.17952260.16514244447097
4.2245-42.380.16492340.16214353458798

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more