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- PDB-8e0a: Crystal structure of human Sar1b -

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Basic information

Entry
Database: PDB / ID: 8e0a
TitleCrystal structure of human Sar1b
ComponentsGTP-binding protein SAR1b
KeywordsSIGNALING PROTEIN / Sar1b / GDP / COPII / small GTPase
Function / homology
Function and homology information


regulation of lipid transport / regulation of COPII vesicle coating / Chylomicron assembly / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / antigen processing and presentation of peptide antigen via MHC class I ...regulation of lipid transport / regulation of COPII vesicle coating / Chylomicron assembly / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / antigen processing and presentation of peptide antigen via MHC class I / COPII-mediated vesicle transport / lipoprotein transport / Golgi cisterna membrane / lipid homeostasis / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / MHC class II antigen presentation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / metal ion binding / cytosol
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'-DIPHOSPHATE / GTP-binding protein SAR1b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 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 SAR1b
B: GTP-binding protein SAR1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,43111
Polymers44,8722
Non-polymers1,5599
Water5,765320
1
A: GTP-binding protein SAR1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2636
Polymers22,4361
Non-polymers8275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein SAR1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1675
Polymers22,4361
Non-polymers7314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.966, 61.485, 70.589
Angle α, β, γ (deg.)90.000, 107.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding protein SAR1b / GTP-binding protein B / GTBPB


Mass: 22435.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAR1B, SARA2, SARB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6B6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2M (NH4)2SO4 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: 0.9778 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 40321 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 32.5
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 5 / Num. unique obs: 2011 / % possible all: 100

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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: 1.797→29.545 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 1997 4.96 %
Rwork0.169 38300 -
obs0.171 40297 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.36 Å2 / Biso mean: 31.9701 Å2 / Biso min: 11.07 Å2
Refinement stepCycle: final / Resolution: 1.797→29.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 91 322 3131
Biso mean--36.24 43.72 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062877
X-RAY DIFFRACTIONf_angle_d1.0423900
X-RAY DIFFRACTIONf_chiral_restr0.064444
X-RAY DIFFRACTIONf_plane_restr0.005475
X-RAY DIFFRACTIONf_dihedral_angle_d18.6931682
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7972-1.84210.2291350.2037263597
1.8421-1.89190.24011490.19662742100
1.8919-1.94760.22091350.18122727100
1.9476-2.01040.21411370.18132737100
2.0104-2.08220.19531590.17252721100
2.0822-2.16560.18281450.16112700100
2.1656-2.26410.20151360.1722767100
2.2641-2.38340.24171470.17092710100
2.3834-2.53270.21541420.17322767100
2.5327-2.72810.2551340.18122740100
2.7281-3.00240.21771440.18952755100
3.0024-3.43630.22191440.1632754100
3.4363-4.32720.17571430.14152775100
4.3272-29.5450.20031470.1703277098
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)
12.4286-0.065-1.46730.86950.29331.213-0.1497-0.0968-0.2030.087-0.0540.07160.1022-0.0370.18190.18910.02480.03120.17240.00090.168466.32452.4697288.883
25.35021.1752-1.57785.2488-0.92496.68080.0184-0.408-0.17920.2292-0.1338-0.52840.16330.3110.09920.16590.034-0.01310.17220.0260.194280.25095.6809288.5259
33.57830.5238-2.67171.6901-0.78163.4435-0.0801-0.0706-0.3620.0321-0.0723-0.1631-0.0150.29020.13350.18870.01770.03440.1772-0.00570.20975.0332-2.2761286.9864
41.15160.51010.39112.40260.72290.884-0.19210.4376-0.2672-0.36820.2024-0.33090.17020.0724-0.00150.248-0.00480.06120.2123-0.03730.183876.67241.3498276.8357
53.73251.79140.43555.26170.290.9544-0.14430.5437-0.0004-1.01150.0129-0.45710.01470.35670.06060.4240.01810.12870.24730.01570.230781.25249.7489270.5485
61.0718-0.4232-0.05111.4638-0.08081.6135-0.07570.22090.0551-0.3952-0.0177-0.1246-0.11750.00890.09510.22740.01150.00970.15590.01920.126675.55714.2265276.3882
74.77292.6144-1.16233.1022-0.7782.715-0.0410.46720.274-0.29170.02250.4049-0.2506-0.1968-0.00460.31870.056-0.0660.28760.07750.229366.435716.481271.747
85.46182.09050.39152.2242-0.91473.22370.18230.8260.1329-0.5873-0.00551.6788-0.3382-1.4435-0.07970.43750.0829-0.2060.55040.03790.653456.96029.1439272.675
94.1539-0.03031.93712.5932-0.06864.5698-0.0958-0.31190.04490.27820.0303-0.0023-0.5621-0.10710.05440.24810.02080.01580.17460.00280.150173.438915.4405286.0928
102.12671.10470.2472.59540.20781.9669-0.07450.00890.23730.0110.03490.343-0.0199-0.15440.010.18740.05670.01930.19480.00850.179163.73048.791284.0044
114.9459-1.39460.84735.8384-3.16275.29390.10040.32710.6032-0.4642-0.2627-1.4671-0.26730.56970.13650.2664-0.04340.10790.3295-0.04430.390563.616917.6897301.1995
122.81471.31-0.62723.38220.44612.43030.1932-0.2660.10850.2191-0.0869-0.1888-0.24520.0215-0.10840.1852-0.00440.00760.1956-0.02510.19753.295218.1849313.6123
130.7598-1.20991.76125.3656-2.14664.23160.00780.04120.4283-0.2684-0.26560.5181-0.1717-0.04040.27020.2880.044-0.04670.2843-0.01460.38240.570522.2727308.7972
141.75040.1818-0.05112.37790.53532.37580.11710.0758-0.1356-0.0957-0.19710.38720.1348-0.39680.0330.1186-0.0171-0.03780.2177-0.04670.226143.03136.2718307.5208
152.10821.6052-2.76991.4522-1.83033.96130.08710.1813-0.1604-0.3953-0.16440.26740.3189-0.57730.06920.29120.0244-0.10150.3113-0.10390.291543.492.0088297.6758
162.83480.14450.00732.28920.05573.38430.18930.4053-0.1684-0.2435-0.0334-0.0897-0.13530.0014-0.15520.15720.0512-0.00170.2131-0.05370.194253.34478.8034298.9935
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 33 )A12 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 45 )A34 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 76 )A46 - 76
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 104 )A77 - 104
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 120 )A105 - 120
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 151 )A121 - 151
7X-RAY DIFFRACTION7chain 'A' and (resid 152 through 161 )A152 - 161
8X-RAY DIFFRACTION8chain 'A' and (resid 162 through 172 )A162 - 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 12 through 25 )B12 - 25
12X-RAY DIFFRACTION12chain 'B' and (resid 26 through 73 )B26 - 73
13X-RAY DIFFRACTION13chain 'B' and (resid 74 through 92 )B74 - 92
14X-RAY DIFFRACTION14chain 'B' and (resid 93 through 150 )B93 - 150
15X-RAY DIFFRACTION15chain 'B' and (resid 151 through 160 )B151 - 160
16X-RAY DIFFRACTION16chain 'B' and (resid 161 through 198 )B161 - 198

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