[English] 日本語
Yorodumi
- PDB-8e0d: Crystal structure of human Sar1bE140D -

+
Open data


ID or keywords:

Loading...

-
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


lipid export from cell / amino acid sensor activity / regulation of COPII vesicle coating / regulation of lipid transport / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / cellular response to leucine starvation / vesicle organization / COPII vesicle coating / COPII vesicle coat ...lipid export from cell / amino acid sensor activity / regulation of COPII vesicle coating / regulation of lipid transport / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / cellular response to leucine starvation / vesicle organization / COPII vesicle coating / COPII vesicle coat / Chylomicron assembly / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / membrane organization / COPII-mediated vesicle transport / Golgi cisterna membrane / lipoprotein transport / lipid homeostasis / endoplasmic reticulum exit site / antigen processing and presentation of peptide antigen via MHC class I / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of TORC1 signaling / MHC class II antigen presentation / small monomeric GTPase / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / G protein activity / lysosomal membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / metal ion 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',3'-TETRAPHOSPHATE / Small COPII coat GTPase 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more