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- PDB-8e0d: Crystal structure of human Sar1bE140D -

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Basic information

Entry
Database: PDB / ID: 8e0d
TitleCrystal structure of human Sar1bE140D
ComponentsGTP-binding protein SAR1b
KeywordsSIGNALING PROTEIN / Sar1b / ppGpp / 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',3'-TETRAPHOSPHATE / GTP-binding protein SAR1b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0252
Polymers22,4221
Non-polymers6031
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.828, 38.420, 55.607
Angle α, β, γ (deg.)90.000, 101.630, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 22421.836 Da / Num. of mol.: 1 / Mutation: E140D
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-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp / Guanosine pentaphosphate


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.32 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.9M 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: 1.98→50 Å / Num. obs: 13267 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.047 / Rrim(I) all: 0.122 / Net I/σ(I): 22
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 644 / CC1/2: 0.951 / CC star: 0.987 / Rpim(I) all: 0.121 / Rrim(I) all: 0.304 / % 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: 1.981→44.481 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 1327 10 %
Rwork0.1567 11938 -
obs0.1611 13265 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.62 Å2 / Biso mean: 23.9562 Å2 / Biso min: 7.93 Å2
Refinement stepCycle: final / Resolution: 1.981→44.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 36 109 1583
Biso mean--29 33.09 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071511
X-RAY DIFFRACTIONf_angle_d0.9582049
X-RAY DIFFRACTIONf_chiral_restr0.057229
X-RAY DIFFRACTIONf_plane_restr0.006255
X-RAY DIFFRACTIONf_dihedral_angle_d17.481886
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9811-2.06040.23481440.1631129498
2.0604-2.15420.19641450.16491310100
2.1542-2.26770.20411470.15671318100
2.2677-2.40980.23381470.16381324100
2.4098-2.59580.21291470.16691328100
2.5958-2.8570.20961450.17471295100
2.857-3.27030.19541490.16151351100
3.2703-4.11980.17631490.13821335100
4.1198-44.480.19421540.1521383100
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)
15.02890.48010.19911.56840.30262.5528-0.0276-0.14170.01380.14310.0251-0.135-0.08740.1914-0.00860.16480.0067-0.01970.102-0.00620.119140.46678.575346.3251
21.45560.8536-0.6189.207-1.47414.7817-0.1951-0.2246-0.2356-0.11380.12590.26650.10280.06260.15320.21390.02090.00530.1412-0.010.127444.519311.9385356.8539
33.7708-3.98580.53914.62990.1091.70580.1360.10460.50870.0232-0.2557-0.0309-0.19990.16280.04230.193-0.009-0.02960.179-0.00830.210138.237820.3204347.0353
43.46631.0368-1.67381.99970.5913.3435-0.0797-0.06850.8362-0.1020.07040.0272-0.5837-0.12710.10770.21770.014-0.02040.0714-0.00870.17536.0316.787340.6384
52.4323-0.0694-0.31591.52710.34881.74180.12590.02910.4685-0.1052-0.01360.0877-0.331-0.0924-0.07730.20560.0102-0.00060.1473-0.00840.179333.594613.1072337.0213
65.91282.7491-2.80084.3007-2.32345.85330.07490.10190.1334-0.0842-0.03190.2246-0.2134-0.354-0.06930.14760.0138-0.06110.1473-0.00520.134322.97468.035333.0261
73.43190.282-0.67421.74631.24021.106-0.12010.25660.0411-0.32740.0119-0.05020.03160.0382-0.00130.0804-0.0179-0.03590.0811-0.00460.080235.79468.5369331.0374
81.65981.14760.87872.7749-1.0327.82890.0628-0.0976-0.16430.04250.03610.17450.5834-1.0304-0.38370.1785-0.0497-0.00490.17160.02980.198723.3726-3.3841340.2339
97.7195-2.3964-0.44731.01150.3491.10670.08070.4959-0.45340.0123-0.06740.05240.18570.039-0.06880.2188-0.00890.00030.1569-0.04560.16135.6523-3.2733329.8253
101.8170.4444-0.90720.9095-0.27993.58060.07360.0462-0.11040.0548-0.0312-0.11140.07660.1822-0.02880.13840.0201-0.01590.10160.00460.117439.950.6813338.2384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 45 )A11 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 55 )A46 - 55
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 66 )A56 - 66
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 85 )A67 - 85
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 104 )A86 - 104
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 119 )A105 - 119
7X-RAY DIFFRACTION7chain 'A' and (resid 120 through 134 )A120 - 134
8X-RAY DIFFRACTION8chain 'A' and (resid 135 through 150 )A135 - 150
9X-RAY DIFFRACTION9chain 'A' and (resid 151 through 164 )A151 - 164
10X-RAY DIFFRACTION10chain 'A' and (resid 165 through 198 )A165 - 198

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