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- PDB-8dzm: Crystal structure of human Sar1a in complex with ppGpp and Magnesium -

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Basic information

Entry
Database: PDB / ID: 8dzm
TitleCrystal structure of human Sar1a in complex with ppGpp and Magnesium
ComponentsGTP-binding protein SAR1a
KeywordsSIGNALING PROTEIN / Sar1a / ppGpp / 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: 1.648 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 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
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

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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)46,0898
Polymers44,7862
Non-polymers1,3046
Water5,080282
1
A: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0454
Polymers22,3931
Non-polymers6523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0454
Polymers22,3931
Non-polymers6523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.125, 35.933, 76.118
Angle α, β, γ (deg.)90.000, 101.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 22392.773 Da / Num. of mol.: 2
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.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% PEG6000 (w/v), 1.0M LiCl, 0.1M MgCl2, 0.1M sodium acetate buffer, pH4.5

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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: 1.64→50 Å / Num. obs: 43805 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rrim(I) all: 0.085 / Net I/σ(I): 18.9
Reflection shellResolution: 1.648→1.68 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 2066 / Rrim(I) all: 0.683 / % possible all: 95.3

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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: 1F6B

1f6b


Resolution: 1.648→45.415 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 2000 4.57 %
Rwork0.1699 41801 -
obs0.1711 43801 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.29 Å2 / Biso mean: 29.7167 Å2 / Biso min: 12.45 Å2
Refinement stepCycle: final / Resolution: 1.648→45.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 76 283 2980
Biso mean--16.83 39.11 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072811
X-RAY DIFFRACTIONf_angle_d0.9563823
X-RAY DIFFRACTIONf_chiral_restr0.056441
X-RAY DIFFRACTIONf_plane_restr0.004469
X-RAY DIFFRACTIONf_dihedral_angle_d18.2241648
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.648-1.68880.29631300.2687273192
1.6888-1.73450.27481420.23032951100
1.7345-1.78550.24551440.20833011100
1.7855-1.84320.22911410.19062948100
1.8432-1.90910.20091450.18433041100
1.9091-1.98550.211430.17052969100
1.9855-2.07590.19951420.15822978100
2.0759-2.18530.19171430.15872997100
2.1853-2.32220.17971440.15773001100
2.3222-2.50150.19441440.16633021100
2.5015-2.75320.20431450.16663023100
2.7532-3.15150.19931440.16333006100
3.1515-3.97020.18981460.1468305399
3.9702-45.410.1731470.1788307197
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)
12.72521.23562.67264.02271.04458.62770.3852-0.2811-0.08410.4739-0.1438-0.2620.36530.2059-0.22790.1375-0.019-0.00930.20170.0040.1648279.078640.531492.9241
27.7091-2.94526.09944.6021-4.11367.88-0.11920.1638-0.02420.08160.0273-0.1688-0.27510.28950.04230.13990.00340.01490.1683-0.02190.1452280.824842.329777.7353
39.3178-0.80612.37783.0605-1.09772.0960.17140.4261-0.1115-0.09350.2505-0.30060.08930.529-0.48870.2196-0.0017-0.00760.1896-0.03690.2259283.803835.195985.0288
42.6935-0.2662-2.32595.9427-1.01182.2703-0.2721-0.0347-0.7278-0.2133-0.07970.22031.24920.33820.27930.36680.0090.01370.2211-0.0120.3375272.551730.105180.5465
52.29041.4081-0.42362.2604-1.37024.48210.07930.1188-0.0408-0.0890.00850.18560.0054-0.1764-0.09330.11770.0433-0.00440.1543-0.01610.1752267.467243.386773.8139
63.52211.167-0.30914.5481-1.06942.70320.0778-0.1597-0.0769-0.0834-0.07980.1094-0.0389-0.1004-0.02090.09720.0344-0.02150.1342-0.02350.1047269.028645.208979.5456
74.08140.3981-1.8781.80590.07896.6458-0.0146-0.01660.24470.0330.15270.2284-0.2585-0.3623-0.11930.12040.065-0.00070.1722-0.02260.2252261.276951.364180.5277
82.37610.3317-1.54325.81860.77962.5973-0.222-0.8457-0.13961.2723-0.4911.311-0.1663-1.33030.60130.41420.06430.14010.71680.00260.406259.286943.63795.6764
99.37560.2769-2.7271.8837-0.80415.511-0.0633-0.060.4551-0.12860.0422-0.1008-0.1754-0.0283-0.10030.19280.0245-0.00450.1172-0.03490.171274.736751.128283.3115
102.16590.6726-2.46522.61760.48136.70190.1327-0.4068-0.16640.161-0.1204-0.16250.0089-0.17510.03580.1509-0.0011-0.03040.22030.00880.1671272.34745.440192.5856
112.31990.47461.06862.67940.7087.20130.1026-0.2370.00440.4651-0.0858-0.3022-0.09150.5423-0.05270.1784-0.042-0.05010.20470.01340.1826307.482263.0277103.5342
122.18470.9117-0.68210.47330.10771.8630.1006-0.2727-0.87230.55030.078-1.00591.81111.2738-0.19850.68440.1827-0.13640.38410.06420.5306308.454449.958599.5876
131.1490.06680.03222.6108-0.31451.626-0.01650.0359-0.06370.1221-0.00410.16070.146-0.11290.01040.1393-0.01410.01170.1108-0.0110.1483293.116456.0394.2094
143.20390.8335-0.94624.2655-2.10715.63630.0424-0.2657-0.0510.4978-0.09780.12070.0883-0.09060.00360.2233-0.00290.03120.1171-0.03270.1162294.180161.4392106.0539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 31 )A13 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 45 )A32 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 73 )A46 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 94 )A74 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 119 )A95 - 119
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 143 )A120 - 143
7X-RAY DIFFRACTION7chain 'A' and (resid 144 through 161 )A144 - 161
8X-RAY DIFFRACTION8chain 'A' and (resid 162 through 171 )A162 - 171
9X-RAY DIFFRACTION9chain 'A' and (resid 172 through 185 )A172 - 185
10X-RAY DIFFRACTION10chain 'A' and (resid 186 through 198 )A186 - 198
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 73 )B13 - 73
12X-RAY DIFFRACTION12chain 'B' and (resid 74 through 94 )B74 - 94
13X-RAY DIFFRACTION13chain 'B' and (resid 95 through 160 )B95 - 160
14X-RAY DIFFRACTION14chain 'B' and (resid 161 through 198 )B161 - 198

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