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- PDB-8e0h: Crystal structure of human Sar1aD104/D140A double mutant -

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Basic information

Entry
Database: PDB / ID: 8e0h
TitleCrystal structure of human Sar1aD104/D140A double mutant
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: 2 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 9, 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)45,8164
Polymers44,6102
Non-polymers1,2062
Water2,990166
1
A: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9082
Polymers22,3051
Non-polymers6031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9082
Polymers22,3051
Non-polymers6031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.534, 61.082, 133.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22304.754 Da / Num. of mol.: 2 / Mutation: D104A, D140A
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-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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 39.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.5M NaCl, 0.2M CaCl2 and 0.1M NaAc, pH4.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 25484 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Net I/σ(I): 32.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1262 / CC1/2: 0.945 / CC star: 0.986 / Rpim(I) all: 0.204 / Rrim(I) all: 0.537 / % 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: 2→45.131 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 1998 7.86 %
Rwork0.182 23409 -
obs0.1857 25407 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.1 Å2 / Biso mean: 44.1134 Å2 / Biso min: 21.3 Å2
Refinement stepCycle: final / Resolution: 2→45.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 72 166 2950
Biso mean--58.15 43.25 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072832
X-RAY DIFFRACTIONf_angle_d0.8723833
X-RAY DIFFRACTIONf_chiral_restr0.054441
X-RAY DIFFRACTIONf_plane_restr0.005462
X-RAY DIFFRACTIONf_dihedral_angle_d18.8111655
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.04980.29981380.23163799
2.0498-2.10520.25011410.20671652100
2.1052-2.16720.27721380.19561618100
2.1672-2.23710.26611420.19331654100
2.2371-2.31710.2631390.19181627100
2.3171-2.40980.23641410.20021656100
2.4098-2.51950.26181440.18671677100
2.5195-2.65230.27491410.20211659100
2.6523-2.81850.2691420.20691651100
2.8185-3.0360.25161420.21121676100
3.036-3.34150.25221440.19421676100
3.3415-3.82480.24051460.16551711100
3.8248-4.8180.16531460.15571717100
4.818-45.1310.19891540.1695179899
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)
10.8924-0.76890.88853.07830.08451.90710.11420.07330.0039-0.4284-0.0317-0.2082-0.1623-0.0532-0.19340.2945-0.01790.04570.25020.01840.2533-0.17041.5066-33.0035
24.62672.30361.13752.6075-1.37043.73090.14140.20390.225-0.138-0.1774-0.3792-0.23310.3413-0.14450.2622-0.01540.06230.39480.02130.29895.50337.7966-24.9412
32.4715-0.7404-1.5492.2172.36896.13460.3893-0.10320.447-0.32610.2274-0.1894-0.21220.512-0.39090.3011-0.01620.05530.25740.02650.29760.08189.1205-29.1452
42.45141.4-1.05552.9465-0.60523.3153-0.1224-0.42190.20170.30650.0565-0.1049-0.0040.14490.00370.38760.02060.0060.3087-0.01760.2857-8.368317.8082-23.1552
50.98340.4162-0.4841.38930.21961.66120.01270.04820.0144-0.1059-0.08840.15210.1447-0.18010.03160.26930.00890.01770.2763-0.00740.272-11.6785.0851-23.3656
61.7573-1.25950.05214.1172-0.90813.6385-0.026-0.2247-0.37780.05940.05520.3660.8986-0.2787-0.01360.3869-0.03540.0390.29140.01610.293-10.2897-8.3153-16.0988
73.77791.10482.39796.5481.69811.7108-0.190.46490.0708-0.6646-0.1720.91970.745-0.74260.20180.3838-0.0864-0.04390.4333-0.01160.5019-18.3058-5.0829-29.9431
83.50681.34214.60690.51591.75966.10060.15240.5378-0.3264-1.7150.04991.11580.1523-0.51740.10330.726-0.0396-0.35860.689-0.02150.5908-20.4779-0.027-38.8747
92.14480.02670.15082.8595-0.19873.6627-0.0420.0916-0.277-0.10190.0623-0.00650.5840.08960.05390.32610.02820.04160.2528-0.05360.2826-5.053-5.1171-30.3259
102.5947-0.4556-0.28512.3528-0.17733.0195-0.0646-0.2395-0.0842-0.15180.0618-0.33550.63120.1195-0.01210.37080.04360.01810.25590.00860.307-17.898-4.70457.5641
113.3557-0.157-0.69594.42551.88784.2986-0.1908-0.54040.0130.6960.2446-0.24360.29670.2584-0.09830.41490.0921-0.01850.4753-0.01340.4769-13.77460.173216.4123
121.4178-0.9165-0.16132.53760.54231.8816-0.0436-0.1006-0.0155-0.18350.0363-0.173-0.1605-0.04710.01060.238-0.04850.01520.2729-0.00440.2643-24.31866.9714.0852
133.28730.0175-0.79262.3595-0.4041.4423-0.25150.5759-0.4252-0.81890.15930.49080.5641-0.8778-0.00040.429-0.128-0.07550.5454-0.02290.4059-35.8616-2.376-0.5277
143.9056-0.0277-1.78223.0569-0.30083.71190.0085-0.1029-0.5664-0.1882-0.0378-0.03820.35990.03670.14730.4432-0.0630.06240.2469-0.01750.3616-22.9232-7.74980.779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 37 )A13 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 62 )A38 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 79 )A63 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 89 )A80 - 89
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 134 )A90 - 134
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 150 )A135 - 150
7X-RAY DIFFRACTION7chain 'A' and (resid 151 through 164 )A151 - 164
8X-RAY DIFFRACTION8chain 'A' and (resid 165 through 172 )A165 - 172
9X-RAY DIFFRACTION9chain 'A' and (resid 173 through 198 )A173 - 198
10X-RAY DIFFRACTION10chain 'B' and (resid 14 through 45 )B14 - 45
11X-RAY DIFFRACTION11chain 'B' and (resid 46 through 66 )B46 - 66
12X-RAY DIFFRACTION12chain 'B' and (resid 67 through 134 )B67 - 134
13X-RAY DIFFRACTION13chain 'B' and (resid 135 through 172 )B135 - 172
14X-RAY DIFFRACTION14chain 'B' and (resid 173 through 198 )B173 - 198

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