[English] 日本語
Yorodumi
- PDB-6o0q: Crystal structure of the TIR domain from human SARM1 in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o0q
TitleCrystal structure of the TIR domain from human SARM1 in complex with ribose
ComponentsSterile alpha and TIR motif-containing protein 1
KeywordsSIGNALING PROTEIN / Axon degeneration
Function / homology
Function and homology information


extrinsic component of synaptic membrane / negative regulation of MyD88-independent toll-like receptor signaling pathway / NADP+ nucleosidase activity / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / NAD+ catabolic process / NAD+ nucleosidase activity / regulation of synapse pruning / modification of postsynaptic structure / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase ...extrinsic component of synaptic membrane / negative regulation of MyD88-independent toll-like receptor signaling pathway / NADP+ nucleosidase activity / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / NAD+ catabolic process / NAD+ nucleosidase activity / regulation of synapse pruning / modification of postsynaptic structure / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / protein localization to mitochondrion / NAD+ nucleosidase activity, cyclic ADP-ribose generating / nervous system process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / regulation of dendrite morphogenesis / response to axon injury / response to glucose / regulation of neuron apoptotic process / signaling adaptor activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / neuromuscular junction / nervous system development / microtubule / mitochondrial outer membrane / cell differentiation / axon / innate immune response / synapse / dendrite / glutamatergic synapse / cell surface / signal transduction / protein-containing complex / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Sterile alpha and TIR motif-containing protein 1 / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Sterile alpha and TIR motif-containing protein 1 / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
beta-D-ribofuranose / NAD(+) hydrolase SARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHorsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Tiancong, Q. / Gilley, J. / Lai, J. / Gu, W. ...Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Tiancong, Q. / Gilley, J. / Lai, J. / Gu, W. / Rank, M. / Deerain, N. / Casey, L. / Ericsson, D.J. / Foley, G. / Hughes, R.O. / Bosanac, T. / von Itzstein, M. / Rathjen, J.P. / Nanson, J.D. / Boden, M. / Dry, I.B. / Williams, S.J. / Staskawicz, B.J. / Coleman, M.P. / Ve, T. / Dodds, P.N. / Kobe, B.
Funding support Australia, 6items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1107804 Australia
National Health and Medical Research Council (NHMRC, Australia)1160570 Australia
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Health and Medical Research Council (NHMRC, Australia)1108859 Australia
Australian Research Council (ARC)DP160102244 Australia
Australian Research Council (ARC)DP190102526 Australia
CitationJournal: Science / Year: 2019
Title: NAD+cleavage activity by animal and plant TIR domains in cell death pathways.
Authors: Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Qi, T. / Gilley, J. / Lai, J.S. / Rank, M.X. / Casey, L.W. / Gu, W. / Ericsson, D.J. / Foley, G. / Hughes, R.O. ...Authors: Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Qi, T. / Gilley, J. / Lai, J.S. / Rank, M.X. / Casey, L.W. / Gu, W. / Ericsson, D.J. / Foley, G. / Hughes, R.O. / Bosanac, T. / von Itzstein, M. / Rathjen, J.P. / Nanson, J.D. / Boden, M. / Dry, I.B. / Williams, S.J. / Staskawicz, B.J. / Coleman, M.P. / Ve, T. / Dodds, P.N. / Kobe, B.
History
DepositionFeb 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sterile alpha and TIR motif-containing protein 1
B: Sterile alpha and TIR motif-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0396
Polymers32,6672
Non-polymers3714
Water3,063170
1
A: Sterile alpha and TIR motif-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5193
Polymers16,3341
Non-polymers1862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sterile alpha and TIR motif-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5193
Polymers16,3341
Non-polymers1862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.986, 86.019, 116.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-977-

HOH

-
Components

#1: Protein Sterile alpha and TIR motif-containing protein 1 / Sterile alpha and Armadillo repeat protein / Sterile alpha motif domain-containing protein 2 / SAM ...Sterile alpha and Armadillo repeat protein / Sterile alpha motif domain-containing protein 2 / SAM domain-containing protein 2 / Tir-1 homolog


Mass: 16333.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SARM1, KIAA0524, SAMD2, SARM / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SZW1
#2: Sugar ChemComp-BDR / beta-D-ribofuranose / beta-D-ribose / D-ribose / ribose / BETA-D-RIBOFURANOSYL


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribofuranoseCOMMON NAMEGMML 1.0
b-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis Tris propane pH 6.5, 0.2 M potassium thiocyanate, 11% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→48.33 Å / Num. obs: 31114 / % possible obs: 98 % / Redundancy: 7.6 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Rrim(I) all: 0.088 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.794 / Num. unique obs: 1803 / CC1/2: 0.884 / Rpim(I) all: 0.299 / Rrim(I) all: 0.843 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
PHENIX(DEV_3357: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.28 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.23
RfactorNum. reflection% reflection
Rfree0.21 1953 6.3 %
Rwork0.172 --
obs0.174 31019 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 22 170 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112362
X-RAY DIFFRACTIONf_angle_d1.0093204
X-RAY DIFFRACTIONf_dihedral_angle_d13.221878
X-RAY DIFFRACTIONf_chiral_restr0.059360
X-RAY DIFFRACTIONf_plane_restr0.008410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.33691350.28682019X-RAY DIFFRACTION96
1.845-1.89490.28861370.25192039X-RAY DIFFRACTION99
1.8949-1.95070.23851350.21711982X-RAY DIFFRACTION94
1.9507-2.01360.27351400.20212066X-RAY DIFFRACTION99
2.0136-2.08560.20091360.17512001X-RAY DIFFRACTION95
2.0856-2.16910.23321380.1772042X-RAY DIFFRACTION98
2.1691-2.26780.19881390.16412042X-RAY DIFFRACTION97
2.2678-2.38740.23011360.16352048X-RAY DIFFRACTION97
2.3874-2.53690.18991400.16682092X-RAY DIFFRACTION98
2.5369-2.73280.21721400.17792088X-RAY DIFFRACTION99
2.7328-3.00780.23261370.17642085X-RAY DIFFRACTION98
3.0078-3.44290.18821420.15932118X-RAY DIFFRACTION99
3.4429-4.33730.15071440.13362157X-RAY DIFFRACTION99
4.3373-48.30130.22461540.18032287X-RAY DIFFRACTION99
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)
13.79892.0318-0.27877.1577-1.94596.56640.0362-0.0081-0.01960.0561-0.0751-0.26030.03090.3726-0.03630.07960.0212-0.00390.21760.01060.176616.528123.657129.5668
23.5963.32490.01515.5702-0.68121.2677-0.0084-0.01250.060.1371-0.06830.00120.23890.32520.09140.21630.049-0.00730.2546-0.00050.218822.267519.840123.8067
35.35430.6223-1.39626.37332.82165.2296-0.22610.4066-0.0441-0.29030.2044-0.4352-0.00210.16720.05040.18720.0204-0.01320.30010.0480.180318.357526.743618.4956
47.8094-0.6535-4.60312.3402-1.09154.70610.64560.33010.65130.1096-0.298-0.3582-1.06210.3064-0.37850.4526-0.05840.03750.27950.0120.32716.692642.179122.4051
56.28531.5727-4.78566.263-1.35593.8020.04010.28280.1695-0.2418-0.032-0.2969-0.221-0.17060.03980.17180.0233-0.01440.23930.04150.180912.707630.676818.9798
64.53890.06350.63892.1549-3.79786.82310.15570.10410.71770.35940.64160.6634-0.9527-1.3344-0.81770.48690.12820.04860.34310.06570.36435.696141.728724.8319
75.63234.5181-3.44885.1190.27618.4144-0.02310.24040.7778-0.00720.27340.4695-0.8594-0.5577-0.42040.34350.06-0.02040.31320.07390.33757.275438.320616.5757
8-0.01570.1529-0.146.3215-5.66734.8491-0.04050.19970.09650.04180.0905-0.04220.1648-0.2461-0.09930.12620.00190.01520.34480.00210.23772.762925.905133.3706
93.6646-0.79893.32878.17980.23343.49490.00350.0362-0.0677-0.39610.1190.14010.5145-0.4645-0.07790.1473-0.05480.02740.2931-0.01980.2213.661218.257428.6111
104.9037-1.14730.13434.67662.30275.4952-0.06110.00770.00880.122-0.05790.23780.0006-0.35940.07450.1237-0.01010.00250.20640.00410.169213.919920.988745.9544
117.7941-5.6601-2.94246.14952.54561.7066-0.1628-0.2584-0.2911-0.0050.10030.17280.1861-0.14640.07620.2383-0.0285-0.01220.33470.01510.20687.953215.80850.1272
125.96670.7645-2.53345.3724-3.1737.184-0.1012-0.4596-0.2580.1103-0.04520.32720.1812-0.23120.07660.1734-0.0291-0.00390.2786-0.04270.139212.057620.331657.3668
137.49320.5051-2.51245.89070.50182.02010.2799-0.94010.89250.5575-0.19280.5058-0.908-0.4384-0.22850.50630.070.02340.4884-0.12630.444713.925936.131858.7775
145.77580.6786-4.31646.4481-1.92273.5081-0.0976-0.13730.170.3535-0.00430.3239-0.1122-0.08410.11430.2063-0.001-0.04030.2936-0.05250.183617.72224.31657.9184
154.7422-0.55911.02917.16155.59314.8299-0.4278-0.25040.2111-0.02170.6871-0.2215-1.05851.8668-0.34210.4288-0.1282-0.06270.435-0.0630.386924.95536.427956.0982
163.2818-3.7985-3.48758.29511.66335.1505-0.2035-0.94211.0859-0.05050.5558-0.3838-0.85570.7963-0.34490.3511-0.0206-0.06320.4682-0.11090.29823.264130.666262.8755
170.4023-0.2172-0.48871.0019-0.30482.01740.05680.09560.13360.02310.1586-0.0752-0.30060.0293-0.14640.18530.0109-0.00050.3387-0.00670.253227.717924.273843.0125
183.7163-1.99133.3998.6422-4.29184.3099-0.09890.0235-0.16040.27260.3225-0.00970.25070.1640.01010.17170.03760.02710.26830.00490.209226.822515.541545.0763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 561 through 586 )
2X-RAY DIFFRACTION2chain 'A' and (resid 587 through 602 )
3X-RAY DIFFRACTION3chain 'A' and (resid 603 through 622 )
4X-RAY DIFFRACTION4chain 'A' and (resid 623 through 637 )
5X-RAY DIFFRACTION5chain 'A' and (resid 638 through 658 )
6X-RAY DIFFRACTION6chain 'A' and (resid 659 through 669 )
7X-RAY DIFFRACTION7chain 'A' and (resid 670 through 677 )
8X-RAY DIFFRACTION8chain 'A' and (resid 678 through 687 )
9X-RAY DIFFRACTION9chain 'A' and (resid 688 through 700 )
10X-RAY DIFFRACTION10chain 'B' and (resid 561 through 586 )
11X-RAY DIFFRACTION11chain 'B' and (resid 587 through 602 )
12X-RAY DIFFRACTION12chain 'B' and (resid 603 through 622 )
13X-RAY DIFFRACTION13chain 'B' and (resid 623 through 637 )
14X-RAY DIFFRACTION14chain 'B' and (resid 638 through 658 )
15X-RAY DIFFRACTION15chain 'B' and (resid 659 through 669 )
16X-RAY DIFFRACTION16chain 'B' and (resid 670 through 677 )
17X-RAY DIFFRACTION17chain 'B' and (resid 678 through 687 )
18X-RAY DIFFRACTION18chain 'B' and (resid 688 through 700 )

+
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