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- PDB-8dzt: Crystal structure of human Sar1aH79G mutant -

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Basic information

Entry
Database: PDB / ID: 8dzt
TitleCrystal structure of human Sar1aH79G mutant
ComponentsGTP-binding protein SAR1a
KeywordsSIGNALING PROTEIN / Sar1a / ppGpp / COPII / small GTPase
Function / homology
Function and homology information


amino acid sensor activity / regulation of COPII vesicle coating / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / cellular response to leucine starvation / vesicle organization / COPII vesicle coating / COPII vesicle coat / membrane organization / Golgi cisterna membrane ...amino acid sensor activity / regulation of COPII vesicle coating / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / cellular response to leucine starvation / vesicle organization / COPII vesicle coating / COPII vesicle coat / membrane organization / Golgi cisterna membrane / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of TORC1 signaling / small monomeric GTPase / intracellular protein transport / G protein activity / lysosomal membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / cytosol
Similarity search - Function
Small GTPase SAR1 domain 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 / Small COPII coat GTPase 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

Downloads & links

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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)46,03910
Polymers44,6232
Non-polymers1,4158
Water8,539474
1
A: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0195
Polymers22,3121
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)23,0195
Polymers22,3121
Non-polymers7084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.718, 55.718, 222.972
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


Mass: 22311.680 Da / Num. of mol.: 2 / Mutation: H79G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR31
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
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: 36062 / % possible obs: 90 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 24.2
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.289 / Num. unique obs: 1515

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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→36.483 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1885 1996 5.53 %
Rwork0.1523 34066 -
obs0.1543 36062 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.85 Å2 / Biso mean: 18.1716 Å2 / Biso min: 5.31 Å2
Refinement stepCycle: final / Resolution: 1.8→36.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 78 475 3135
Biso mean--9.58 31.68 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062717
X-RAY DIFFRACTIONf_angle_d0.9193680
X-RAY DIFFRACTIONf_chiral_restr0.06417
X-RAY DIFFRACTIONf_plane_restr0.004451
X-RAY DIFFRACTIONf_dihedral_angle_d17.3361582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8002-1.84520.20611450.17752425
1.8452-1.89510.19691400.16372429
1.8951-1.95080.20051410.152409
1.9508-2.01380.18341430.14972434
2.0138-2.08580.18251410.15032432
2.0858-2.16930.19941430.15432446
2.1693-2.2680.17531360.14992436
2.268-2.38750.1961470.15032431
2.3875-2.53710.18321480.14242432
2.5371-2.73290.18221420.15372423
2.7329-3.00780.17621460.15732441
3.0078-3.44270.1931340.14442442
3.4427-4.33640.17981420.13542456
4.3364-36.4830.20161480.17422430
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)
14.34930.01370.192.74030.04953.5090.1211-0.03320.3596-0.0328-0.21960.801-0.2857-0.56750.10960.1130.03840.01940.1928-0.03530.240619.1727-1.974110.3315
22.1573-0.559-0.63862.41681.55713.44390.0370.02070.1003-0.1673-0.15870.1498-0.2407-0.22560.03890.06680.0292-0.00880.06090.0040.128.7101-5.3286-3.6186
30.5344-1.0814-0.64572.86170.87581.36960.1061-0.02810.2447-0.147-0.0723-0.3666-0.16760.097-0.0170.07090.0130.00910.09420.00230.145435.1071-2.9876-0.7667
41.99170.01480.09911.77750.47651.41860.0185-0.1250.08190.044-0.0072-0.22330.01020.103-0.0280.06420.0228-0.00330.07890.02470.10839.3306-13.4761.654
51.8960.18180.34131.72040.56261.6094-0.0152-0.1666-0.08120.1526-0.00680.06690.14-0.00060.03620.07970.00780.02470.08750.02950.070628.4279-17.50234.2268
64.1562-0.0675-0.72864.4035-0.37553.6002-0.1537-0.1701-0.3816-0.194-0.0346-0.75440.34180.58170.11630.12680.04650.04370.1601-0.00880.234844.467915.6079-4.069
71.8391-0.1006-0.8151.4009-0.29242.0554-0.0539-0.18870.05840.0022-0.0112-0.24170.09590.24110.06150.04960.0168-0.00410.10110.00050.094236.787822.25259.8178
85.2857-0.7871-2.00631.68050.88093.3576-0.1182-0.48990.08140.12810.1237-0.07550.11930.2772-0.0430.07970.00450.00770.10660.00380.102940.761526.51137.3896
94.7121.0563-0.28220.3228-0.42131.4678-0.0158-0.37351.35560.10780.1010.0282-0.68740.021-0.1070.14840.0229-0.02060.0966-0.03370.414432.806437.61827.9404
101.1801-0.35470.26930.62280.60031.11950.00340.02030.1706-0.1207-0.0617-0.0885-0.11590.02870.02870.06320.02740.00310.07150.00550.087630.809224.79585.5454
112.33420.406-1.09643.2449-2.53514.03220.0539-0.07070.2137-0.0053-0.03640.0873-0.00520.0251-0.05450.05690.0095-0.01030.0814-0.03940.113921.204326.82279.7156
122.28280.4081-0.82611.8967-0.2461.82790.02370.18120.3044-0.5280.04280.05140.0513-0.0760.02260.07440.0214-0.00930.1090.0240.111527.787528.0645-1.2974
131.2554-0.5529-0.33253.0102-1.30661.1038-0.01120.1527-0.1259-0.10680.04960.21240.0487-0.2544-0.01340.07240.0037-0.01520.1376-0.04240.104220.570416.7413.5378
142.6643-0.08170.48912.8758-1.14684.21890.03250.0024-0.1917-0.03660.0682-0.17330.06630.0296-0.07770.05220.00830.00870.0777-0.01580.077930.290412.5145.4894
152.3979-0.11110.23042.5111-0.5033.4339-0.09840.4034-0.2283-0.2710.0316-0.18080.0982-0.0303-0.05590.10840.04110.03280.1053-0.04180.092334.777216.9036-4.632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 25 )A14 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 46 )A26 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 104 )A47 - 104
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 134 )A105 - 134
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 198 )A135 - 198
6X-RAY DIFFRACTION6chain 'B' and (resid 14 through 25 )B14 - 25
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 46 )B26 - 46
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 79 )B47 - 79
9X-RAY DIFFRACTION9chain 'B' and (resid 80 through 89 )B80 - 89
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 104 )B90 - 104
11X-RAY DIFFRACTION11chain 'B' and (resid 105 through 119 )B105 - 119
12X-RAY DIFFRACTION12chain 'B' and (resid 120 through 134 )B120 - 134
13X-RAY DIFFRACTION13chain 'B' and (resid 135 through 172 )B135 - 172
14X-RAY DIFFRACTION14chain 'B' and (resid 173 through 185 )B173 - 185
15X-RAY DIFFRACTION15chain 'B' and (resid 186 through 198 )B186 - 198

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