[English] 日本語
Yorodumi
- PDB-8dzm: Crystal structure of human Sar1a in complex with ppGpp and Magnesium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dzm
TitleCrystal structure of human Sar1a in complex with ppGpp and Magnesium
ComponentsGTP-binding protein SAR1a
KeywordsSIGNALING PROTEIN / Sar1a / ppGpp / 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',3'-TETRAPHOSPHATE / Small COPII coat GTPase SAR1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.648 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP-binding protein SAR1a
B: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0898
Polymers44,7862
Non-polymers1,3046
Water5,080282
1
A: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0454
Polymers22,3931
Non-polymers6523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0454
Polymers22,3931
Non-polymers6523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.125, 35.933, 76.118
Angle α, β, γ (deg.)90.000, 101.520, 90.000
Int Tables number5
Space group name H-MC121

-
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% PEG6000 (w/v), 1.0M LiCl, 0.1M MgCl2, 0.1M sodium acetate buffer, pH4.5

-
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 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 43805 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rrim(I) all: 0.085 / Net I/σ(I): 18.9
Reflection shellResolution: 1.648→1.68 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 2066 / Rrim(I) all: 0.683 / % possible all: 95.3

-
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: 1F6B

1f6b


Resolution: 1.648→45.415 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 2000 4.57 %
Rwork0.1699 41801 -
obs0.1711 43801 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.29 Å2 / Biso mean: 29.7167 Å2 / Biso min: 12.45 Å2
Refinement stepCycle: final / Resolution: 1.648→45.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 76 283 2980
Biso mean--16.83 39.11 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072811
X-RAY DIFFRACTIONf_angle_d0.9563823
X-RAY DIFFRACTIONf_chiral_restr0.056441
X-RAY DIFFRACTIONf_plane_restr0.004469
X-RAY DIFFRACTIONf_dihedral_angle_d18.2241648
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.648-1.68880.29631300.2687273192
1.6888-1.73450.27481420.23032951100
1.7345-1.78550.24551440.20833011100
1.7855-1.84320.22911410.19062948100
1.8432-1.90910.20091450.18433041100
1.9091-1.98550.211430.17052969100
1.9855-2.07590.19951420.15822978100
2.0759-2.18530.19171430.15872997100
2.1853-2.32220.17971440.15773001100
2.3222-2.50150.19441440.16633021100
2.5015-2.75320.20431450.16663023100
2.7532-3.15150.19931440.16333006100
3.1515-3.97020.18981460.1468305399
3.9702-45.410.1731470.1788307197
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)
12.72521.23562.67264.02271.04458.62770.3852-0.2811-0.08410.4739-0.1438-0.2620.36530.2059-0.22790.1375-0.019-0.00930.20170.0040.1648279.078640.531492.9241
27.7091-2.94526.09944.6021-4.11367.88-0.11920.1638-0.02420.08160.0273-0.1688-0.27510.28950.04230.13990.00340.01490.1683-0.02190.1452280.824842.329777.7353
39.3178-0.80612.37783.0605-1.09772.0960.17140.4261-0.1115-0.09350.2505-0.30060.08930.529-0.48870.2196-0.0017-0.00760.1896-0.03690.2259283.803835.195985.0288
42.6935-0.2662-2.32595.9427-1.01182.2703-0.2721-0.0347-0.7278-0.2133-0.07970.22031.24920.33820.27930.36680.0090.01370.2211-0.0120.3375272.551730.105180.5465
52.29041.4081-0.42362.2604-1.37024.48210.07930.1188-0.0408-0.0890.00850.18560.0054-0.1764-0.09330.11770.0433-0.00440.1543-0.01610.1752267.467243.386773.8139
63.52211.167-0.30914.5481-1.06942.70320.0778-0.1597-0.0769-0.0834-0.07980.1094-0.0389-0.1004-0.02090.09720.0344-0.02150.1342-0.02350.1047269.028645.208979.5456
74.08140.3981-1.8781.80590.07896.6458-0.0146-0.01660.24470.0330.15270.2284-0.2585-0.3623-0.11930.12040.065-0.00070.1722-0.02260.2252261.276951.364180.5277
82.37610.3317-1.54325.81860.77962.5973-0.222-0.8457-0.13961.2723-0.4911.311-0.1663-1.33030.60130.41420.06430.14010.71680.00260.406259.286943.63795.6764
99.37560.2769-2.7271.8837-0.80415.511-0.0633-0.060.4551-0.12860.0422-0.1008-0.1754-0.0283-0.10030.19280.0245-0.00450.1172-0.03490.171274.736751.128283.3115
102.16590.6726-2.46522.61760.48136.70190.1327-0.4068-0.16640.161-0.1204-0.16250.0089-0.17510.03580.1509-0.0011-0.03040.22030.00880.1671272.34745.440192.5856
112.31990.47461.06862.67940.7087.20130.1026-0.2370.00440.4651-0.0858-0.3022-0.09150.5423-0.05270.1784-0.042-0.05010.20470.01340.1826307.482263.0277103.5342
122.18470.9117-0.68210.47330.10771.8630.1006-0.2727-0.87230.55030.078-1.00591.81111.2738-0.19850.68440.1827-0.13640.38410.06420.5306308.454449.958599.5876
131.1490.06680.03222.6108-0.31451.626-0.01650.0359-0.06370.1221-0.00410.16070.146-0.11290.01040.1393-0.01410.01170.1108-0.0110.1483293.116456.0394.2094
143.20390.8335-0.94624.2655-2.10715.63630.0424-0.2657-0.0510.4978-0.09780.12070.0883-0.09060.00360.2233-0.00290.03120.1171-0.03270.1162294.180161.4392106.0539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 31 )A13 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 45 )A32 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 73 )A46 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 94 )A74 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 119 )A95 - 119
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 143 )A120 - 143
7X-RAY DIFFRACTION7chain 'A' and (resid 144 through 161 )A144 - 161
8X-RAY DIFFRACTION8chain 'A' and (resid 162 through 171 )A162 - 171
9X-RAY DIFFRACTION9chain 'A' and (resid 172 through 185 )A172 - 185
10X-RAY DIFFRACTION10chain 'A' and (resid 186 through 198 )A186 - 198
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 73 )B13 - 73
12X-RAY DIFFRACTION12chain 'B' and (resid 74 through 94 )B74 - 94
13X-RAY DIFFRACTION13chain 'B' and (resid 95 through 160 )B95 - 160
14X-RAY DIFFRACTION14chain 'B' and (resid 161 through 198 )B161 - 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