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- PDB-8dzn: Crystal structure of human Sar1a in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 8dzn
TitleCrystal structure of human Sar1a in complex with GDP
ComponentsGTP-binding protein SAR1a
KeywordsSIGNALING PROTEIN / Sar1a / GDP / 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'-DIPHOSPHATE / Small COPII coat GTPase SAR1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.107 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

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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)45,7685
Polymers44,7862
Non-polymers9823
Water2,180121
1
A: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8362
Polymers22,3931
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9323
Polymers22,3931
Non-polymers5392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.172, 63.970, 62.233
Angle α, β, γ (deg.)90.000, 105.950, 90.000
Int Tables number4
Space group name H-MP1211

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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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5M NaH2PO4/K2HPO4 and 0.1M sodium citrate, pH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 24060 / % possible obs: 95.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.066 / Rrim(I) all: 0.136 / Net I/σ(I): 17.57
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 1138 / CC1/2: 0.951 / Rpim(I) all: 0.159 / Rrim(I) all: 0.324 / % possible all: 88.7

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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: 2.107→28.208 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1993 8.31 %
Rwork0.1806 21992 -
obs0.1852 23985 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.92 Å2 / Biso mean: 43.8389 Å2 / Biso min: 21.48 Å2
Refinement stepCycle: final / Resolution: 2.107→28.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 0 61 121 2902
Biso mean--42.56 45.6 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072836
X-RAY DIFFRACTIONf_angle_d1.0223843
X-RAY DIFFRACTIONf_chiral_restr0.059448
X-RAY DIFFRACTIONf_plane_restr0.006469
X-RAY DIFFRACTIONf_dihedral_angle_d17.7811665
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1071-2.15980.34851310.2315144487
2.1598-2.21820.25251390.2219153493
2.2182-2.28340.27721380.2192153395
2.2834-2.35710.27291420.1913157697
2.3571-2.44130.27931430.1986160098
2.4413-2.5390.28061470.1985160398
2.539-2.65440.26461440.2048160198
2.6544-2.79430.25291480.1938162098
2.7943-2.96910.27871470.1975162899
2.9691-3.19810.2471460.1903160298
3.1981-3.51940.22811450.1713158397
3.5194-4.02740.18711400.1541155694
4.0274-5.06930.1771390.1424153292
5.0693-28.20.23361440.1864158093
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)
11.448-1.1127-0.70431.91812.61277.0541-0.0752-0.16150.4341-0.0903-0.12852.10860.0218-1.3024-0.01990.34320.02510.00340.53840.06020.5822-85.64878.113-90.4055
25.6304-1.447-1.24943.40740.40234.67430.06980.4892-0.1366-0.41440.01510.27960.2702-0.1672-0.08790.3089-0.0161-0.06680.19680.03950.2227-71.37917.3502-100.3638
32.9688-0.7679-0.40755.3012-0.56582.0440.29381.05160.2636-1.010.06420.1241-0.07990.2587-0.14350.56260.0051-0.01440.5478-0.07160.4678-73.32699.9033-109.9888
48.2036-1.5878-3.31933.00260.3124.94740.16730.16110.5176-0.23670.17590.0285-0.33-0.3072-0.32360.45260.0246-0.08330.2153-0.00230.2812-74.928314.2255-97.1773
52.59390.92190.15221.5545-0.63461.4202-0.06-0.03440.0648-0.4536-0.0764-0.0128-0.21130.170.07030.4528-0.0004-0.1490.19950.010.2996-65.04219.5389-94.7891
63.791-0.27220.00213.85230.42913.2960.229-0.1636-0.19270.0664-0.0977-0.5860.01920.2654-0.07290.3828-0.0104-0.12790.20080.03660.3652-60.86242.7616-92.5192
74.721-0.15234.18793.6613-0.55874.43440.24840.3146-0.4773-0.5320.1911-0.18110.44130.3038-0.48670.50260.0241-0.07520.2282-0.02570.376-65.6293-9.8681-98.8547
85.4627-0.2363-1.21193.67210.80782.14530.1409-0.66-0.32860.3077-0.0352-0.13060.18320.294-0.17420.440.0015-0.10460.32030.05780.2443-68.6518-2.2738-79.8299
96.7684-0.25023.65964.4631-0.48962.32580.338-0.0818-0.4182-0.45550.16580.28320.4418-0.5077-0.61190.312-0.0175-0.11340.2530.01740.3035-74.9249-3.8435-96.9502
108.41212.44373.92787.54572.69162.2289-0.2048-0.5449-0.1239-0.268-0.06230.6169-0.3419-0.47330.23140.2350.02-0.00790.28010.05440.2184-77.57832.4577-87.2588
114.4609-0.1532-1.77266.97051.47216.4216-0.07810.0870.0675-0.3766-0.0947-0.1068-0.3586-0.03380.30370.2344-0.08310.00960.2795-0.01420.2108-84.0239-5.4344-82.0014
124.4634-1.7459-0.46932.8462-0.27194.1543-0.03070.0697-0.2136-0.31140.09930.4621-0.1098-0.3607-0.03770.3633-0.0322-0.12890.2063-0.02160.2622-100.0378-4.7629-74.7391
138.34721.8966-3.66472.3932-0.40763.7275-0.12550.7483-0.0375-0.28950.19290.58680.1213-0.621-0.20440.4749-0.0186-0.13060.31820.01720.3469-99.4955-10.1501-77.917
141.16321.6453-0.22464.3157-1.0060.40980.0948-0.028-0.52640.5902-0.0254-0.46940.30110.1350.0990.76740.0218-0.1190.2799-0.01470.3106-96.7842-12.9688-64.3876
153.3082-0.464-0.69512.9561-0.13642.5584-0.1105-0.06110.04750.50440.05530.2767-0.2283-0.14520.01420.45220.0136-0.05350.19330.00330.2766-99.29530.7634-63.7377
160.53210.0793-1.39643.39420.60637.5065-0.09930.04630.6132-0.1286-0.04630.545-1.6374-0.55420.23970.55340.068-0.11710.23560.00860.356-102.29712.6745-69.5915
173.2278-0.2425-3.45325.5887-1.10883.94180.0394-0.63750.09330.2303-0.2074-0.8504-0.27590.49380.15160.4957-0.0977-0.1950.3618-0.01320.2993-84.03275.7716-62.3237
189.7265-0.72554.54934.41370.5587.8888-0.05850.75690.4296-0.4494-0.0013-0.0798-0.85640.2240.15670.5269-0.01570.00850.23840.0490.2732-95.91376.5181-76.434
197.90670.72272.4693.94260.01268.2582-0.1309-0.18290.27230.08190.0276-0.2920.0097-0.05430.15350.2649-0.0415-0.0280.22560.01180.2124-85.88540.4301-73.7671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 25 )A13 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 44 )A26 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 61 )A45 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 75 )A62 - 75
5X-RAY DIFFRACTION5chain 'A' and (resid 76 through 104 )A76 - 104
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 134 )A105 - 134
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 151 )A135 - 151
8X-RAY DIFFRACTION8chain 'A' and (resid 152 through 172 )A152 - 172
9X-RAY DIFFRACTION9chain 'A' and (resid 173 through 185 )A173 - 185
10X-RAY DIFFRACTION10chain 'A' and (resid 186 through 198 )A186 - 198
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 25 )B13 - 25
12X-RAY DIFFRACTION12chain 'B' and (resid 26 through 44 )B26 - 44
13X-RAY DIFFRACTION13chain 'B' and (resid 45 through 75 )B45 - 75
14X-RAY DIFFRACTION14chain 'B' and (resid 76 through 94 )B76 - 94
15X-RAY DIFFRACTION15chain 'B' and (resid 95 through 134 )B95 - 134
16X-RAY DIFFRACTION16chain 'B' and (resid 135 through 151 )B135 - 151
17X-RAY DIFFRACTION17chain 'B' and (resid 152 through 172 )B152 - 172
18X-RAY DIFFRACTION18chain 'B' and (resid 173 through 185 )B173 - 185
19X-RAY DIFFRACTION19chain 'B' and (resid 186 through 198 )B186 - 198

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