PDB-8p8h: Crystal structure of HHD2 domain of hRTEL1

ID or keywords:

Entry

Database: PDB / ID: 8p8h

Title

Crystal structure of HHD2 domain of hRTEL1

Components

Regulator of telomere elongation helicase 1

Keywords

DNA BINDING PROTEIN / Helicase / HHD2 domain

Function / homology

Function and homology information

DNA strand displacement / telomeric loop disassembly / negative regulation of telomere maintenance in response to DNA damage / positive regulation of telomeric loop disassembly / Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / positive regulation of telomere maintenance via telomere lengthening / negative regulation of t-circle formation / Cytosolic iron-sulfur cluster assembly / mitotic telomere maintenance via semi-conservative replication / negative regulation of DNA recombination ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Hegde, R.P. / Kanade, M. / Cortone, G. / Graewert, M. / Longo, A. / Gonzalez, A. / Chaves-Arquero, B. / Blanco, F.J. / Napolitano, L.M.R. / Onesti, S.

Funding support

Italy, European Union, 2items

Citation

Journal: To Be Published
Title: Crystal structure of HHD2 domain of hRTEL1
Authors: Hegde, R.P. / Kanade, M. / Cortone, G. / Graewert, M. / Longo, A. / Gonzalez, A. / Chaves-Arquero, B. / Blanco, F.J. / Napolitano, L.M.R. / Onesti, S.

History

Deposition	Jun 1, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 12, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8p8h.cif.gz	283.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8p8h.ent.gz	178.5 KB	Display	PDB format
PDBx/mmJSON format	8p8h.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/p8/8p8h ftp://data.pdbj.org/pub/pdb/validation_reports/p8/8p8h	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	SASBDB: SASDRZ9associated SAS data SASBDB: SASDRV9associated SAS data SASBDB: SASDRW9associated SAS data SASBDB: SASDRX9associated SAS data SASBDB: SASDRY9associated SAS data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#172 - Apr 2014 RecA and Rad51 similarity (1) #236 - Aug 2019 Cyclin and Cyclin-dependent Kinase similarity (1)

Deposited unit

A: Regulator of telomere elongation helicase 1

B: Regulator of telomere elongation helicase 1

C: Regulator of telomere elongation helicase 1

D: Regulator of telomere elongation helicase 1

E: Regulator of telomere elongation helicase 1

F: Regulator of telomere elongation helicase 1

G: Regulator of telomere elongation helicase 1

73.9 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	65.590, 60.680, 79.530
Angle α, β, γ (deg.)	90.000, 96.130, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	7 - 82
2	1	1	A	7 - 82
3	2	2	A	7 - 83
4	2	2	A	7 - 83
5	3	3	A	7 - 83
6	3	3	A	7 - 83
7	4	4	A	7 - 82
8	4	4	A	7 - 82
9	5	5	A	7 - 83
10	5	5	A	7 - 83
11	6	6	A	7 - 83
12	6	6	A	7 - 83
13	7	7	A	6 - 82
14	7	7	A	6 - 82
15	8	8	A	6 - 82
16	8	8	A	6 - 82
17	9	9	A	6 - 82
18	9	9	A	6 - 82
19	10	10	A	6 - 82
20	10	10	A	6 - 82
21	11	11	A	6 - 82
22	11	11	A	6 - 82
23	12	12	A	6 - 84
24	12	12	A	6 - 84
25	13	13	A	6 - 82
26	13	13	A	6 - 82
27	14	14	A	6 - 83
28	14	14	A	6 - 83
29	15	15	A	6 - 83
30	15	15	A	6 - 83
31	16	16	A	6 - 82
32	16	16	A	6 - 82
33	17	17	A	6 - 83
34	17	17	A	6 - 83
35	18	18	A	6 - 83
36	18	18	A	6 - 83
37	19	19	A	6 - 82
38	19	19	A	6 - 82
39	20	20	A	6 - 82
40	20	20	A	6 - 82
41	21	21	A	6 - 85
42	21	21	A	6 - 85

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

#1: Protein	Regulator of telomere elongation helicase 1 / Novel helicase-like Mass: 10557.053 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RTEL1, C20orf41, KIAA1088, NHL / Production host: Escherichia coli B (bacteria) / References: UniProt: Q9NZ71, DNA helicase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.24 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CHES pH 9.5, 30% PEG 3000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 27255 / % possible obs: 97.9 % / Redundancy: 6 % / CC_1/2: 0.997 / Net I/σ(I): 10.53
Reflection shell	Resolution: 2.3→2.44 Å / Mean I/σ(I) obs: 1.99 / Num. unique obs: 4294 / CC_1/2: 0.836 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→48.14 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.928 / SU B: 19.306 / SU ML: 0.218 / Cross valid method: FREE R-VALUE / ESU R: 0.353 / ESU R Free: 0.246
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.257	1363	5.002 %
R_work	0.2142	25886	-
all	0.216	-	-
obs	-	27249	97.849 %

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 47.233 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.476 Å²	-0 Å²	1.373 Å²
2-	-	-0.901 Å²	0 Å²
3-	-	-	-0.85 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→48.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4188	0	0	60	4248

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	4301
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4079
X-RAY DIFFRACTION	r_angle_refined_deg	1.887	1.651	5840
X-RAY DIFFRACTION	r_angle_other_deg	0.624	1.585	9362
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.116	5	552
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.701	5	27
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.476	10	681
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.234	10	177
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	692
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	5029
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	967
X-RAY DIFFRACTION	r_nbd_refined	0.249	0.2	970
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	3325
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	2276
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	2394
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.129	0.2	102
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.175	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.266	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	2.235	2.627	2220
X-RAY DIFFRACTION	r_mcbond_other	2.232	2.626	2219
X-RAY DIFFRACTION	r_mcangle_it	3.402	4.705	2768
X-RAY DIFFRACTION	r_mcangle_other	3.402	4.705	2769
X-RAY DIFFRACTION	r_scbond_it	2.669	2.986	2081
X-RAY DIFFRACTION	r_scbond_other	2.669	2.987	2082
X-RAY DIFFRACTION	r_scangle_it	4.176	5.346	3072
X-RAY DIFFRACTION	r_scangle_other	4.175	5.347	3073
X-RAY DIFFRACTION	r_lrange_it	6.576	32.365	18280
X-RAY DIFFRACTION	r_lrange_other	6.576	32.363	18263
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.104	0.05	2373
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.096	0.05	2387
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.103	0.05	2368
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.1	0.05	2356
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.092	0.05	2414
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.08	0.05	2453
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.109	0.05	2392
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.082	0.05	2439
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.113	0.05	2369
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.095	0.05	2410
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.099	0.05	2403
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.107	0.05	2378
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.098	0.05	2343
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.067	0.05	2412
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.082	0.05	2381
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.11	0.05	2318
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.095	0.05	2381
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.112	0.05	2384
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.103	0.05	2339
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.104	0.05	2365
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.073	0.05	2499

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10399	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10399	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.0959	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.0959	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10302	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.10302	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.09966	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.09966	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.0924	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.0924	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07984	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07984	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.10875	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.10875	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.08192	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.08192	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.11341	0.05008
9	18	A	X-RAY DIFFRACTION	Local ncs	0.11341	0.05008
10	19	A	X-RAY DIFFRACTION	Local ncs	0.09521	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.09521	0.05009
11	21	A	X-RAY DIFFRACTION	Local ncs	0.09896	0.05009
11	22	A	X-RAY DIFFRACTION	Local ncs	0.09896	0.05009
12	23	A	X-RAY DIFFRACTION	Local ncs	0.10666	0.05009
12	24	A	X-RAY DIFFRACTION	Local ncs	0.10666	0.05009
13	25	A	X-RAY DIFFRACTION	Local ncs	0.0984	0.05009
13	26	A	X-RAY DIFFRACTION	Local ncs	0.0984	0.05009
14	27	A	X-RAY DIFFRACTION	Local ncs	0.06655	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.06655	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.08206	0.05009
15	30	A	X-RAY DIFFRACTION	Local ncs	0.08206	0.05009
16	31	A	X-RAY DIFFRACTION	Local ncs	0.11039	0.05008
16	32	A	X-RAY DIFFRACTION	Local ncs	0.11039	0.05008
17	33	A	X-RAY DIFFRACTION	Local ncs	0.09545	0.05009
17	34	A	X-RAY DIFFRACTION	Local ncs	0.09545	0.05009
18	35	A	X-RAY DIFFRACTION	Local ncs	0.11155	0.05009
18	36	A	X-RAY DIFFRACTION	Local ncs	0.11155	0.05009
19	37	A	X-RAY DIFFRACTION	Local ncs	0.10287	0.05009
19	38	A	X-RAY DIFFRACTION	Local ncs	0.10287	0.05009
20	39	A	X-RAY DIFFRACTION	Local ncs	0.10417	0.05009
20	40	A	X-RAY DIFFRACTION	Local ncs	0.10417	0.05009
21	41	A	X-RAY DIFFRACTION	Local ncs	0.07261	0.05009
21	42	A	X-RAY DIFFRACTION	Local ncs	0.07261	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.3-2.36	0.288	98	0.297	1866	0.297	2024	0.945	0.942	97.0356	0.265
2.36-2.424	0.344	96	0.29	1815	0.293	2015	0.917	0.947	94.8387	0.251
2.424-2.494	0.32	94	0.271	1783	0.274	1912	0.944	0.955	98.1695	0.233
2.494-2.571	0.325	91	0.255	1739	0.259	1872	0.943	0.961	97.7564	0.218
2.571-2.655	0.291	90	0.244	1696	0.246	1829	0.947	0.966	97.649	0.204
2.655-2.748	0.373	86	0.246	1638	0.252	1768	0.926	0.966	97.5113	0.208
2.748-2.851	0.255	83	0.238	1591	0.239	1711	0.962	0.966	97.8375	0.201
2.851-2.967	0.312	81	0.222	1526	0.226	1632	0.941	0.971	98.4681	0.186
2.967-3.098	0.253	78	0.218	1481	0.22	1582	0.964	0.973	98.5461	0.189
3.098-3.249	0.251	73	0.214	1402	0.216	1501	0.96	0.973	98.2678	0.192
3.249-3.424	0.279	71	0.228	1344	0.231	1440	0.959	0.971	98.2639	0.207
3.424-3.63	0.296	68	0.209	1278	0.213	1369	0.942	0.976	98.3199	0.197
3.63-3.88	0.244	63	0.204	1203	0.207	1290	0.971	0.978	98.1395	0.194
3.88-4.188	0.194	58	0.174	1114	0.175	1185	0.975	0.984	98.903	0.164
4.188-4.584	0.242	55	0.168	1037	0.172	1103	0.959	0.984	99.0027	0.164
4.584-5.12	0.179	49	0.181	936	0.181	1003	0.984	0.982	98.2054	0.181
5.12-5.901	0.308	45	0.223	840	0.227	895	0.961	0.976	98.8827	0.212
5.901-7.2	0.277	37	0.258	713	0.259	759	0.944	0.97	98.8142	0.238
7.2-10.07	0.182	29	0.155	558	0.156	598	0.98	0.987	98.1605	0.182
10.07-48.14	0.212	18	0.213	326	0.213	357	0.974	0.972	96.3585	0.26

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.6728	0.215	-0.7865	6.4043	-0.3973	0.7211	-0.1266	-0.5218	-0.1379	0.3438	0.0835	-0.0683	-0.1088	0.4201	0.0432	0.1216	0.0162	0.0365	0.4521	0.0041	0.0756	-9.512	24.049	7.083
2	1.8375	0.9312	-0.6933	1.9591	0.5343	1.9221	0.09	0.1285	0.1702	0.0202	-0.0236	0.0084	-0.0358	-0.1576	-0.0664	0.0227	0.0147	0.047	0.2592	0.0079	0.1012	8.912	-0.489	12.732
3	3.4209	-0.8711	-1.7826	1.1365	-0.2391	2.8804	0.1776	-0.6297	-0.1937	-0.3303	-0.028	0.118	-0.4259	0.4809	-0.1497	0.3149	-0.0126	0.0566	0.3169	-0.0107	0.0793	19.579	29.465	37.056
4	1.8629	-0.816	-0.2593	0.7368	-0.1175	2.0758	-0.2028	0.002	-0.1752	0.2587	0.0606	0.1536	0.0601	0.1451	0.1421	0.1502	0.0314	0.1299	0.2534	-0.0218	0.1509	1.151	46.514	26.572
5	5.0374	0.7846	-1.0757	4.3979	2.5513	1.9798	-0.4478	-0.8169	-0.636	0.0626	-0.0511	0.3521	0.2183	0.3041	0.4989	0.1564	0.1899	0.2338	0.4913	0.3705	0.4009	10.958	15.895	49.737
6	1.3261	1.0454	0.3266	3.245	0.3757	1.6733	0.0441	0.1259	0.0106	-0.0969	-0.0114	0.1594	-0.0886	0.0867	-0.0327	0.0863	-0.0053	0.0875	0.2462	-0.0065	0.1312	21.558	22.476	17.23
7	3.103	0.15	0.7503	2.0956	-1.0041	2.8156	0.0274	-0.2606	-0.3278	-0.2068	-0.2231	-0.2198	-0.0028	0.0032	0.1957	0.0809	-0.0077	0.0767	0.3303	0.0464	0.1609	39.491	11.766	13.034

Refinement TLS group

Selection: ALL

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About Yorodumi

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Yorodumi