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- PDB-6x90: Structure of the guanine nucleotide exchange factor Sec12 bound t... -

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Basic information

Entry
Database: PDB / ID: 6x90
TitleStructure of the guanine nucleotide exchange factor Sec12 bound to the small GTPase Sar1
Components
  • Guanine nucleotide-exchange factor SEC12
  • Small COPII coat GTPase SAR1
KeywordsPROTEIN TRANSPORT / Endoplasmic reticulum / GTPase / exchange factor / membrane trafficking
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 / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-mediated vesicle transport / nuclear envelope organization / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum ...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 / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-mediated vesicle transport / nuclear envelope organization / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / mitochondrial fission / mitochondrial membrane organization / endoplasmic reticulum exit site / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / GTPase activator activity / guanyl-nucleotide exchange factor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / mitochondrion
Similarity search - Function
Guanine nucleotide-exchange factor Sec12-like / 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 / WD40 repeats / WD40 repeat ...Guanine nucleotide-exchange factor Sec12-like / 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 / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Guanine nucleotide-exchange factor SEC12 / Small COPII coat GTPase SAR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsJoiner, A.M.N. / Fromme, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098621 United States
CitationJournal: Structure / Year: 2021
Title: Structural basis for the initiation of COPII vesicle biogenesis.
Authors: Joiner, A.M.N. / Fromme, J.C.
History
DepositionJun 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Guanine nucleotide-exchange factor SEC12
A: Small COPII coat GTPase SAR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0053
Polymers58,9662
Non-polymers391
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-10 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.333, 93.620, 115.423
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 39369.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SEC12, SED2, YNR026C, N3244 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11655
#2: Protein Small COPII coat GTPase SAR1 / GTP-binding protein SAR1 / Secretion-associated RAS-related protein 1


Mass: 19596.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SAR1, YPL218W / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P20606, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 5mg/mL protein, 100mM MES pH6.5, 30% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.26→57.71 Å / Num. obs: 20215 / % possible obs: 95.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 49.22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 20.1
Reflection shellResolution: 2.26→2.33 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1012 / CC1/2: 0.854 / Rpim(I) all: 0.313 / Rrim(I) all: 0.806 / % possible all: 98.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
STARANISOdata scaling
Cootmodel building
PHENIX1.18.2_3874+SVNrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H5I, 1F6B

4h5i

1f6b


Resolution: 2.26→57.71 Å / SU ML: 0.3257 / Cross valid method: FREE R-VALUE / Phase error: 32.2202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2556 922 4.56 %
Rwork0.1986 19282 -
obs0.2013 20204 76.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.16 Å2
Refinement stepCycle: LAST / Resolution: 2.26→57.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 1 72 3826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523814
X-RAY DIFFRACTIONf_angle_d0.7845155
X-RAY DIFFRACTIONf_chiral_restr0.0527606
X-RAY DIFFRACTIONf_plane_restr0.0041656
X-RAY DIFFRACTIONf_dihedral_angle_d17.63861393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.380.3465780.29411580X-RAY DIFFRACTION44.82
2.38-2.520.3615880.27451841X-RAY DIFFRACTION51.88
2.52-2.720.3602830.26992229X-RAY DIFFRACTION62.59
2.72-2.990.26841220.26972789X-RAY DIFFRACTION78.04
2.99-3.430.30681600.22883490X-RAY DIFFRACTION97.02
3.43-4.320.25051810.18143602X-RAY DIFFRACTION99.58
4.32-57.710.21922100.1653751X-RAY DIFFRACTION99.62
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.69361048556-0.3534647644660.2306869426795.35552386624-1.262113022763.864480917350.07723542277270.0306793192476-0.136259493695-0.141736923450.2025711813641.43562456065-0.0295951353849-0.976380996652-0.2543575482860.299411411082-0.0330723184183-0.004433089829280.565669823664-0.03475577365550.654693002281112.18444548912.974488119331.1093722341
22.698214851470.8757786595880.09963231580245.995197741260.3222478767075.604440614380.0588248720760.606256314018-0.0520542645835-1.37642143849-0.02760743145630.2906222479970.259177554746-0.344527932753-0.04092090917810.5842448674440.0568087199798-0.07757261751240.424017180535-0.005569618314640.395859316907123.54455667917.144529442415.1442360393
35.080448023222.15214618663-2.615509135863.4264278386-0.2381008958845.745507945770.415581924984-0.05558014655671.141164761831.342940640750.4043230127890.687077746932-1.25991942108-0.863145589284-0.6789050144190.7015905793880.1302099622080.1148656113130.3744775410540.005769608812560.459620273478125.06593348820.775352743851.1882098436
47.65756642639-2.50134913484-0.4150210851974.853447325460.4563633195218.511749700420.510280161423-0.9739264041991.850032136491.50903907888-0.6450620744930.00440452044321-1.38983814356-0.6089705127420.0827859468120.776693935319-0.008936293021770.1556306040690.463807154464-0.1508073667270.658591482889128.63226034426.109710572646.9888282149
52.2616832108-0.1397493260312.978216765418.14926450316-4.72826573046.12559731688-0.1334642906430.0535660110392-0.09038448342360.3016444450880.0744727666958-0.08516031615280.1221145800490.1305993483660.1234705471060.2197742434950.05315160849130.06155322130140.313442613265-0.08162975433020.320892186136130.61481353213.657086843441.1364936724
68.430632296040.202360378058-5.215073622756.61530659634-2.192317034059.961734191880.09065309960890.162250853228-1.047038043380.1613690646-0.236379844671-0.3214377410261.107641355730.578576961171-0.1404861113650.4595407147170.0957391964205-0.1438243958860.418866399566-0.07664930095140.530032519942133.4354253376.9377377809347.708054681
77.70715202324-2.63302863785-3.164605198139.425438773761.88915285154.83566979772-0.162976825461-1.43072493097-0.09146269883611.258191350560.346145557454-0.464504329801-0.05483664313240.965820734454-0.1796890427650.57080558481-0.0422910420006-0.09017069062960.607379474248-0.00489168405930.356970057537134.67613187914.403078132459.1636997574
88.87768756913.67156848793-2.155350472038.965119809790.43611068261210.00055481270.69802317333-0.3641887099150.4570739422120.543407759084-0.3249264101510.222774029814-2.242359533681.03944665567-0.5846907066331.03948547891-0.0981468068309-0.1101914410610.553166452944-0.1137942203960.435614453407140.75266495926.060967449951.2624347912
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 144 )BA1 - 1441 - 144
22chain 'B' and (resid 145 through 344 )BA145 - 344145 - 344
33chain 'A' and (resid 24 through 44 )AC24 - 441 - 21
44chain 'A' and (resid 45 through 76 )AC45 - 7622 - 34
55chain 'A' and (resid 77 through 102 )AC77 - 10235 - 60
66chain 'A' and (resid 103 through 125 )AC103 - 12561 - 83
77chain 'A' and (resid 126 through 178 )AC126 - 17884 - 126
88chain 'A' and (resid 179 through 193 )AC179 - 193127 - 141

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