PDB-8p2m: C. elegans TIR-1 protein.

ID or keywords:

Entry

Database: PDB / ID: 8p2m

Title

C. elegans TIR-1 protein.

Components

NAD(+) hydrolase tir-1

Keywords

HYDROLASE /

SARM1 / TIR-1 /

C. elegans /

neurodegeneration /

cryo-EM /

structural biology / NAD+ metabolism / axon Wallerian degeneration

Function / homology

Function and homology information

serotonin biosynthetic process / negative regulation of MyD88-independent toll-like receptor signaling pathway / NAD catabolic process /

NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / cell fate specification / response to axon injury / defense response to fungus ...
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

ELECTRON MICROSCOPY /

single particle reconstruction /

cryo EM / Resolution: 3.82 Å

Authors

Isupov, M.N. / Opatowsky, Y.

Funding support

Israel,

United States, 3items

Citation

Journal: Cell Rep / Year: 2023
Title: Structure-function analysis of ceTIR-1/hSARM1 explains the lack of Wallerian axonal degeneration in C. elegans.
Authors: Tami Khazma / Atira Grossman / Julia Guez-Haddad / Chengye Feng / Hadas Dabas / Radhika Sain / Michal Weitman / Ran Zalk / Michail N Isupov / Marc Hammarlund / Michael Hons / Yarden Opatowsky /

Abstract: Wallerian axonal degeneration (WD) does not occur in the nematode C. elegans, in contrast to other model animals. However, WD depends on the NADase activity of SARM1, a protein that is also expressed ...

History

Deposition	May 16, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 6, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8p2m.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb8p2m.ent.gz	872.3 KB	Display	PDB format
PDBx/mmJSON format	8p2m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p2/8p2m ftp://data.pdbj.org/pub/pdb/validation_reports/p2/8p2m	HTTPS FTP

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Related structure data

Related structure data	17370MC 17369C 8p2lC M: map data used to model this data C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (5)

Deposited unit

A: NAD(+) hydrolase tir-1

B: NAD(+) hydrolase tir-1

C: NAD(+) hydrolase tir-1

D: NAD(+) hydrolase tir-1

E: NAD(+) hydrolase tir-1

F: NAD(+) hydrolase tir-1

G: NAD(+) hydrolase tir-1

H: NAD(+) hydrolase tir-1

I: NAD(+) hydrolase tir-1

760 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 194 - 849 / Label seq-ID: 60 - 715

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56
29	Local NCS retraints between domains: 57 58
30	Local NCS retraints between domains: 59 60
31	Local NCS retraints between domains: 61 62
32	Local NCS retraints between domains: 63 64
33	Local NCS retraints between domains: 65 66
34	Local NCS retraints between domains: 67 68
35	Local NCS retraints between domains: 69 70
36	Local NCS retraints between domains: 71 72

#1: Protein	NAD(+) hydrolase tir-1 / NADase tir-1 / Neuronal symmetry protein 2 / SARM1 homolog / Sterile alpha and TIR motif-containing ...NADase tir-1 / Neuronal symmetry protein 2 / SARM1 homolog / Sterile alpha and TIR motif-containing protein tir-1 Mass: 84496.172 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tir-1, nsy-2, F13B10.1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) References: UniProt: Q86DA5, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase

#1: Protein

NAD(+) hydrolase tir-1 / NADase tir-1 / Neuronal symmetry protein 2 / SARM1 homolog / Sterile alpha and TIR motif-containing ...

Mass: 84496.172 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Caenorhabditis elegans (invertebrata) / Gene: tir-1, nsy-2, F13B10.1 / Cell line (production host): HEK293F / Production host:

Homo sapiens (human)
References: UniProt: Q86DA5, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase

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Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component	Name: C. elegans TIR1. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)	Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)	Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solution	pH: 8.5
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support	Grid type: Quantifoil R1.2/1.3
Vitrification	Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Model: TFS KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recording	Electron dose: 41.4 e/Å² / Film or detector model: GATAN K3 (6k x 4k)
EM imaging optics	Energyfilter name: GIF Quantum LS

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Processing

Software

Name: REFMAC / Version: 5.8.0267 / Classification: refinement

EM software

ID	Name	Version	Category
2	EPU		image acquisition
7	Coot	9.6	model fitting
8	ISOLDE	1.5	model fitting
10	cryoSPARC		initial Euler assignment
11	cryoSPARC		final Euler assignment
20	REFMAC	5	model refinement
21	UCSF ChimeraX	1.5	model refinement
22	ISOLDE	1.5	model refinement

CTF correction

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

Particle selection

Num. of particles selected: 370021

3D reconstruction

Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121487 / Algorithm: FOURIER SPACE / Symmetry type: POINT

Atomic model building

Protocol: FLEXIBLE FIT / Space: RECIPROCAL

Atomic model building

Source name: AlphaFold / Type: in silico model

Refinement

Resolution: 3.82→3.82 Å / Cor.coef. F_o:F_c: 0.916 / WR_factor R_work: 0.449 / SU B: 72.443 / SU ML: 0.838 / Average fsc overall: 0.4155 / Average fsc work: 0.4155 / ESU R: 0.503 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_work	0.4491	729964	-
all	0.449	-	-
R_free	-	-	0 %
obs	-	-	100 %

Solvent computation

Solvent model: BABINET MODEL

Displacement parameters

B_iso mean: 349.919 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.548 Å²	0.574 Å²	-0.05 Å²
2-	-	1.071 Å²	1.45 Å²
3-	-	-	-0.523 Å²

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
ELECTRON MICROSCOPY	r_bond_refined_d	0.01	0.012	47586
ELECTRON MICROSCOPY	r_angle_refined_deg	1.834	1.632	64269
ELECTRON MICROSCOPY	r_dihedral_angle_1_deg	7.033	5	5802
ELECTRON MICROSCOPY	r_dihedral_angle_2_deg	32.533	23.123	2408
ELECTRON MICROSCOPY	r_dihedral_angle_3_deg	14.068	15	8976
ELECTRON MICROSCOPY	r_dihedral_angle_4_deg	19.338	15	252
ELECTRON MICROSCOPY	r_chiral_restr	0.14	0.2	6332
ELECTRON MICROSCOPY	r_gen_planes_refined	0.014	0.02	35067
ELECTRON MICROSCOPY	r_nbd_refined	0.206	0.2	51528
ELECTRON MICROSCOPY	r_nbtor_refined	0.292	0.2	66676
ELECTRON MICROSCOPY	r_xyhbond_nbd_refined	0.082	0.2	4102
ELECTRON MICROSCOPY	r_mcbond_it	10.522	34.364	23259
ELECTRON MICROSCOPY	r_mcangle_it	17.83	51.526	29044
ELECTRON MICROSCOPY	r_scbond_it	14.708	35.431	24327
ELECTRON MICROSCOPY	r_scangle_it	24.411	52.768	35225
ELECTRON MICROSCOPY	r_lrange_it	42.699	655.086	212861
ELECTRON MICROSCOPY	r_ncsr_local_group_1	0.134	0.05	42672
ELECTRON MICROSCOPY	r_ncsr_local_group_2	0.139	0.05	42164
ELECTRON MICROSCOPY	r_ncsr_local_group_3	0.13	0.05	42402
ELECTRON MICROSCOPY	r_ncsr_local_group_4	0.137	0.05	42328
ELECTRON MICROSCOPY	r_ncsr_local_group_5	0.138	0.05	42238
ELECTRON MICROSCOPY	r_ncsr_local_group_6	0.131	0.05	42566
ELECTRON MICROSCOPY	r_ncsr_local_group_7	0.132	0.05	42576
ELECTRON MICROSCOPY	r_ncsr_local_group_8	0.13	0.05	42426
ELECTRON MICROSCOPY	r_ncsr_local_group_9	0.11	0.05	44266
ELECTRON MICROSCOPY	r_ncsr_local_group_10	0.094	0.05	44640
ELECTRON MICROSCOPY	r_ncsr_local_group_11	0.1	0.05	44768
ELECTRON MICROSCOPY	r_ncsr_local_group_12	0.105	0.05	44360
ELECTRON MICROSCOPY	r_ncsr_local_group_13	0.091	0.05	45094
ELECTRON MICROSCOPY	r_ncsr_local_group_14	0.09	0.05	44848
ELECTRON MICROSCOPY	r_ncsr_local_group_15	0.098	0.05	44540
ELECTRON MICROSCOPY	r_ncsr_local_group_16	0.108	0.05	44056
ELECTRON MICROSCOPY	r_ncsr_local_group_17	0.112	0.05	43968
ELECTRON MICROSCOPY	r_ncsr_local_group_18	0.114	0.05	43710
ELECTRON MICROSCOPY	r_ncsr_local_group_19	0.107	0.05	44284
ELECTRON MICROSCOPY	r_ncsr_local_group_20	0.107	0.05	44236
ELECTRON MICROSCOPY	r_ncsr_local_group_21	0.109	0.05	44048
ELECTRON MICROSCOPY	r_ncsr_local_group_22	0.098	0.05	44452
ELECTRON MICROSCOPY	r_ncsr_local_group_23	0.102	0.05	44182
ELECTRON MICROSCOPY	r_ncsr_local_group_24	0.093	0.05	44558
ELECTRON MICROSCOPY	r_ncsr_local_group_25	0.087	0.05	44746
ELECTRON MICROSCOPY	r_ncsr_local_group_26	0.1	0.05	44110
ELECTRON MICROSCOPY	r_ncsr_local_group_27	0.105	0.05	44156
ELECTRON MICROSCOPY	r_ncsr_local_group_28	0.1	0.05	44402
ELECTRON MICROSCOPY	r_ncsr_local_group_29	0.097	0.05	44424
ELECTRON MICROSCOPY	r_ncsr_local_group_30	0.103	0.05	44094
ELECTRON MICROSCOPY	r_ncsr_local_group_31	0.101	0.05	44396
ELECTRON MICROSCOPY	r_ncsr_local_group_32	0.099	0.05	44290
ELECTRON MICROSCOPY	r_ncsr_local_group_33	0.11	0.05	43812
ELECTRON MICROSCOPY	r_ncsr_local_group_34	0.084	0.05	44918
ELECTRON MICROSCOPY	r_ncsr_local_group_35	0.093	0.05	44512
ELECTRON MICROSCOPY	r_ncsr_local_group_36	0.09	0.05	44628

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	ELECTRON MICROSCOPY	Local ncs	0.1336	0.05009
1	2	B	ELECTRON MICROSCOPY	Local ncs	0.1336	0.05009
2	3	A	ELECTRON MICROSCOPY	Local ncs	0.13869	0.05009
2	4	C	ELECTRON MICROSCOPY	Local ncs	0.13869	0.05009
3	5	A	ELECTRON MICROSCOPY	Local ncs	0.12989	0.05009
3	6	D	ELECTRON MICROSCOPY	Local ncs	0.12989	0.05009
4	7	A	ELECTRON MICROSCOPY	Local ncs	0.1368	0.05009
4	8	E	ELECTRON MICROSCOPY	Local ncs	0.1368	0.05009
5	9	A	ELECTRON MICROSCOPY	Local ncs	0.13819	0.05009
5	10	F	ELECTRON MICROSCOPY	Local ncs	0.13819	0.05009
6	11	A	ELECTRON MICROSCOPY	Local ncs	0.13121	0.05009
6	12	G	ELECTRON MICROSCOPY	Local ncs	0.13121	0.05009
7	13	A	ELECTRON MICROSCOPY	Local ncs	0.1317	0.05009
7	14	H	ELECTRON MICROSCOPY	Local ncs	0.1317	0.05009
8	15	A	ELECTRON MICROSCOPY	Local ncs	0.12991	0.05009
8	16	I	ELECTRON MICROSCOPY	Local ncs	0.12991	0.05009
9	17	B	ELECTRON MICROSCOPY	Local ncs	0.11035	0.0501
9	18	C	ELECTRON MICROSCOPY	Local ncs	0.11035	0.0501
10	19	B	ELECTRON MICROSCOPY	Local ncs	0.09372	0.0501
10	20	D	ELECTRON MICROSCOPY	Local ncs	0.09372	0.0501
11	21	B	ELECTRON MICROSCOPY	Local ncs	0.09973	0.0501
11	22	E	ELECTRON MICROSCOPY	Local ncs	0.09973	0.0501
12	23	B	ELECTRON MICROSCOPY	Local ncs	0.10452	0.0501
12	24	F	ELECTRON MICROSCOPY	Local ncs	0.10452	0.0501
13	25	B	ELECTRON MICROSCOPY	Local ncs	0.09087	0.05011
13	26	G	ELECTRON MICROSCOPY	Local ncs	0.09087	0.05011
14	27	B	ELECTRON MICROSCOPY	Local ncs	0.09035	0.0501
14	28	H	ELECTRON MICROSCOPY	Local ncs	0.09035	0.0501
15	29	B	ELECTRON MICROSCOPY	Local ncs	0.09762	0.0501
15	30	I	ELECTRON MICROSCOPY	Local ncs	0.09762	0.0501
16	31	C	ELECTRON MICROSCOPY	Local ncs	0.10813	0.0501
16	32	D	ELECTRON MICROSCOPY	Local ncs	0.10813	0.0501
17	33	C	ELECTRON MICROSCOPY	Local ncs	0.11232	0.0501
17	34	E	ELECTRON MICROSCOPY	Local ncs	0.11232	0.0501
18	35	C	ELECTRON MICROSCOPY	Local ncs	0.11443	0.0501
18	36	F	ELECTRON MICROSCOPY	Local ncs	0.11443	0.0501
19	37	C	ELECTRON MICROSCOPY	Local ncs	0.10717	0.0501
19	38	G	ELECTRON MICROSCOPY	Local ncs	0.10717	0.0501
20	39	C	ELECTRON MICROSCOPY	Local ncs	0.10715	0.0501
20	40	H	ELECTRON MICROSCOPY	Local ncs	0.10715	0.0501
21	41	C	ELECTRON MICROSCOPY	Local ncs	0.10892	0.0501
21	42	I	ELECTRON MICROSCOPY	Local ncs	0.10892	0.0501
22	43	D	ELECTRON MICROSCOPY	Local ncs	0.09811	0.0501
22	44	E	ELECTRON MICROSCOPY	Local ncs	0.09811	0.0501
23	45	D	ELECTRON MICROSCOPY	Local ncs	0.1021	0.0501
23	46	F	ELECTRON MICROSCOPY	Local ncs	0.1021	0.0501
24	47	D	ELECTRON MICROSCOPY	Local ncs	0.09252	0.0501
24	48	G	ELECTRON MICROSCOPY	Local ncs	0.09252	0.0501
25	49	D	ELECTRON MICROSCOPY	Local ncs	0.08734	0.0501
25	50	H	ELECTRON MICROSCOPY	Local ncs	0.08734	0.0501
26	51	D	ELECTRON MICROSCOPY	Local ncs	0.10006	0.0501
26	52	I	ELECTRON MICROSCOPY	Local ncs	0.10006	0.0501
27	53	E	ELECTRON MICROSCOPY	Local ncs	0.10483	0.0501
27	54	F	ELECTRON MICROSCOPY	Local ncs	0.10483	0.0501
28	55	E	ELECTRON MICROSCOPY	Local ncs	0.09951	0.0501
28	56	G	ELECTRON MICROSCOPY	Local ncs	0.09951	0.0501
29	57	E	ELECTRON MICROSCOPY	Local ncs	0.09723	0.0501
29	58	H	ELECTRON MICROSCOPY	Local ncs	0.09723	0.0501
30	59	E	ELECTRON MICROSCOPY	Local ncs	0.10343	0.0501
30	60	I	ELECTRON MICROSCOPY	Local ncs	0.10343	0.0501
31	61	F	ELECTRON MICROSCOPY	Local ncs	0.10084	0.0501
31	62	G	ELECTRON MICROSCOPY	Local ncs	0.10084	0.0501
32	63	F	ELECTRON MICROSCOPY	Local ncs	0.09947	0.0501
32	64	H	ELECTRON MICROSCOPY	Local ncs	0.09947	0.0501
33	65	F	ELECTRON MICROSCOPY	Local ncs	0.11028	0.0501
33	66	I	ELECTRON MICROSCOPY	Local ncs	0.11028	0.0501
34	67	G	ELECTRON MICROSCOPY	Local ncs	0.08415	0.05011
34	68	H	ELECTRON MICROSCOPY	Local ncs	0.08415	0.05011
35	69	G	ELECTRON MICROSCOPY	Local ncs	0.09285	0.0501
35	70	I	ELECTRON MICROSCOPY	Local ncs	0.09285	0.0501
36	71	H	ELECTRON MICROSCOPY	Local ncs	0.09038	0.0501
36	72	I	ELECTRON MICROSCOPY	Local ncs	0.09038	0.0501

LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection R_free: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc work	WR_factor R_work
3.821-3.92	0.857	54640	0.857	54640	0.118	0.857
3.92-4.027	0.709	52348	0.709	52348	0.131	0.709
4.027-4.144	0.631	51442	0.631	51442	0.161	0.631
4.144-4.271	0.587	49864	0.587	49864	0.208	0.587
4.271-4.411	0.559	48232	0.559	48232	0.252	0.559
4.411-4.566	0.55	46130	0.55	46130	0.308	0.55
4.566-4.739	0.536	45316	0.536	45316	0.37	0.536
4.739-4.932	0.529	42742	0.529	42742	0.384	0.529
4.932-5.151	0.516	41818	0.516	41818	0.433	0.516
5.151-5.403	0.5	39347	0.5	39347	0.494	0.5
5.403-5.695	0.494	37666	0.494	37666	0.518	0.494
5.695-6.04	0.487	35777	0.487	35777	0.538	0.487
6.04-6.457	0.482	33541	0.482	33541	0.553	0.482
6.457-6.974	0.449	31037	0.449	31037	0.617	0.449
6.974-7.639	0.411	28679	0.411	28679	0.731	0.411
7.639-8.54	0.403	25856	0.403	25856	0.8	0.403
8.54-9.859	0.398	23118	0.398	23118	0.836	0.398
9.859-12.071	0.357	19263	0.357	19263	0.867	0.357
12.071-17.053	0.344	14961	0.344	14961	0.841	0.344
17.053-268.8	0.43	8184	0.43	8184	0.915	0.43

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