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- PDB-8dzo: Crystal structure of human Sar1T39N mutant -

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Basic information

Entry
Database: PDB / ID: 8dzo
TitleCrystal structure of human Sar1T39N mutant
ComponentsGTP-binding protein SAR1a
KeywordsSIGNALING PROTEIN / Sar1 / Sar1a / COPII / small GTPase
Function / homology
Function and homology information


regulation of COPII vesicle coating / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / intracellular protein transport / GTPase activity ...regulation of COPII vesicle coating / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / intracellular protein transport / GTPase activity / GTP binding / Golgi apparatus
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / GTP-binding protein SAR1a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHuang, Q.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM040654 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 CA163255 United States
CitationJournal: Proteins / Year: 2023
Title: The alarmone ppGpp selectively inhibits the isoform A of the human small GTPase Sar1.
Authors: Huang, Q. / Szebenyi, D.M.E.
History
DepositionAug 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 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

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Assembly

Deposited unit
A: GTP-binding protein SAR1a
B: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,27110
Polymers44,8402
Non-polymers1,4318
Water6,666370
1
A: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1275
Polymers22,4201
Non-polymers7084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1435
Polymers22,4201
Non-polymers7234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.605, 55.605, 222.404
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein GTP-binding protein SAR1a / COPII-associated small GTPase


Mass: 22419.799 Da / Num. of mol.: 2 / Mutation: T39N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAR1A, SAR1, SARA, SARA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR31
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp / Guanosine pentaphosphate


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% PEG3350 (w/v), 0.1M CaCl2, 0.1M Mes-HCl buffer, pH6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35856 / % possible obs: 99.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 36.64
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 12.16 / Num. unique obs: 1756 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DZM

8dzm


Resolution: 1.8→36.401 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1932 1994 5.58 %
Rwork0.1595 33770 -
obs0.1613 35764 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.66 Å2 / Biso mean: 24.0932 Å2 / Biso min: 5.7 Å2
Refinement stepCycle: final / Resolution: 1.8→36.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 78 371 2982
Biso mean--15.17 34.37 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062681
X-RAY DIFFRACTIONf_angle_d0.923630
X-RAY DIFFRACTIONf_chiral_restr0.057413
X-RAY DIFFRACTIONf_plane_restr0.004441
X-RAY DIFFRACTIONf_dihedral_angle_d17.1861566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8003-1.84530.22241410.17412389100
1.8453-1.89520.22761440.15492424100
1.8952-1.9510.20971440.15252393100
1.951-2.01390.19821480.15522425100
2.0139-2.08590.18811380.14982409100
2.0859-2.16940.18491460.15882425100
2.1694-2.26810.18761420.15872416100
2.2681-2.38770.20121400.16332406100
2.3877-2.53730.18841410.15942450100
2.5373-2.73310.19081380.1662384100
2.7331-3.0080.18871480.17192409100
3.008-3.4430.20341460.15782450100
3.443-4.33670.15751400.14762410100
4.3367-36.4010.22191380.1663238098
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)
10.313-0.25870.01220.2104-0.00790.153-0.03190.0343-0.11170.11580.0164-0.05770.16230.0676-0.00070.08190.00810.01920.0602-0.0130.099436.4558-24.2778-10.5039
20.2152-0.13340.21720.4013-0.01960.2539-0.02680.0330.08270.02590.0059-0.1798-0.01830.1321-0.00010.13380.00680.01470.152-0.00610.17342.114-17.0635-7.8278
30.1882-0.20030.04060.4174-0.19520.115-0.05220.02090.153-0.02780.0195-0.23320.04930.0161-0.00050.1592-0.00450.0130.13950.01460.181234.9309-7.3891-9.3649
40.9310.28610.19160.60590.09260.29760.00020.1277-0.0514-0.1398-0.03120.1457-0.0305-0.1027-0.00020.16240.015-0.01530.1246-0.00190.11926.3814-14.7464-12.4405
50.58170.62350.02670.65110.0030.3685-0.0348-0.05460.0158-0.08120.0029-0.1109-0.12750.1305-0.00010.14440.0007-0.01330.1463-0.00220.167768.5297-26.3957-13.0499
61.04180.3326-0.11910.907-0.04990.4499-0.0072-0.0891-0.03340.0974-0.03440.02760.0403-0.0513-0.00010.1482-0.00220.00430.11990.00030.118357.4057-35.7088-11.693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 45 )A14 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 104 )A46 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 134 )A105 - 134
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 198 )A135 - 198
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 94 )B13 - 94
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 198 )B95 - 198

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