PDB-6f4t: Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-14...

ID or keywords:

Entry

Database: PDB / ID: 6f4t

Title

Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)

Components

JmjC domain-containing protein 5
RCC1 domain-containing protein 1

Keywords

OXIDOREDUCTASE / NON-HEME /

IRON /

2-OXOGLUTARATE /

DIOXYGENASE / JMJC / JMJC DOMAIN / Lysine-specific demethylase 8 / JmjC domain-containing protein 5 / Arginyl C-3 Hydroxylase / JMJD5 /

KDM8 /

OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING /

TRANSLATION / DSBH / FACIAL TRIAD /

CYTOPLASM / JMJC HYDROXYLASE / JMJC DEMETHYLASE /

KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM /

BETA-HYDROXYLATION /

HYDROXYLATION / ARGININE HYDROXYLATION / RCC1 domain-containing protein 1 / RCCD1 / Regulator of chromosome condensation /

40S ribosomal protein S6 /

RPS6 /

RIBOSOME BIOGENESIS /

TRANSCRIPTION /

EPIGENETIC REGULATION /

SIGNALING / DEVELOPMENT / CELL STRUCTURE / TRANSCRIPTION ACTIVATOR/INHIBITOR /

PHOSPHORYLATION /

CANCER / POLYMORPHISM

Function / homology

Function and homology information

[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity /

Hydrolases; Acting on peptide bonds (peptidases) /

Protein hydroxylation /

aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.22 Å

Authors

Chowdhury, R. / Islam, M.S. / Schofield, C.J.

Citation

Journal: Nat Commun / Year: 2018
Title: JMJD5 is a human arginyl C-3 hydroxylase.
Authors: Wilkins, S.E. / Islam, S. / Gannon, J.M. / Markolovic, S. / Hopkinson, R.J. / Ge, W. / Schofield, C.J. / Chowdhury, R.

History

Deposition	Nov 30, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 4, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6f4t.cif.gz	179.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6f4t.ent.gz	144 KB	Display	PDB format
PDBx/mmJSON format	6f4t.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f4/6f4t ftp://data.pdbj.org/pub/pdb/validation_reports/f4/6f4t	HTTPS FTP

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Related structure data

Related structure data	6f4mC 6f4nC 6f4oC 6f4pC 6f4qC 6f4rSC 6f4sC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6f4r-1 6i9l-d 6f4p-d 6i9m-d 6i9n-d 6f4q-1 4gaz-1 4upg-d 4gjz-d 4qu1-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#234 - Jun 2019 MDM2 and Cancer similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (6)

Deposited unit

A: JmjC domain-containing protein 5

B: RCC1 domain-containing protein 1

hetero molecules

30.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: JmjC domain-containing protein 5

hetero molecules

defined by author
Evidence: gel filtration
30.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: RCC1 domain-containing protein 1

defined by author
584 Da, 1 polymers

Unit cell

Length a, b, c (Å)	49.137, 65.169, 78.446
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein	JmjC domain-containing protein 5 / Jumonji domain-containing protein 5 / Lysine-specific demethylase 8 Mass: 29471.150 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 183-416 / Mutation: C217A, C232A, W414C Source method: isolated from a genetically manipulated source Details: FRAGMENT: 183-416 / Source: (gene. exp.) Homo sapiens (human) / Gene: KDM8, JMJD5 / Plasmid: PNIC28 BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8N371, [50S ribosomal protein L16]-arginine 3-hydroxylase
#2: Protein/peptide	RCC1 domain-containing protein 1 Mass: 583.681 Da / Num. of mol.: 1 / Fragment: UNP residues 139-143 / Source method: obtained synthetically / Details: FRAGMENT: 139-143 / Source: (synth.) Homo sapiens (human) / References: UniProt: A6NED2

#1: Protein

JmjC domain-containing protein 5 / Jumonji domain-containing protein 5 / Lysine-specific demethylase 8

Mass: 29471.150 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 183-416 / Mutation: C217A, C232A, W414C
Source method: isolated from a genetically manipulated source
Details: FRAGMENT: 183-416 / Source: (gene. exp.)

Homo sapiens (human) / Gene: KDM8, JMJD5 / Plasmid: PNIC28 BSA4 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8N371, [50S ribosomal protein L16]-arginine 3-hydroxylase

#2: Protein/peptide

RCC1 domain-containing protein 1

Mass: 583.681 Da / Num. of mol.: 1 / Fragment: UNP residues 139-143 / Source method: obtained synthetically / Details: FRAGMENT: 139-143 / Source: (synth.)

Homo sapiens (human) / References: UniProt: A6NED2

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Non-polymers , 5 types, 344 molecules

#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₅NO₅ / Comment: inhibitor*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.3 Å³/Da / Density % sol: 46.64 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 17.1 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2017 / Details: MIRRORS
Radiation	Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.22→50.13 Å / Num. obs: 75316 / % possible obs: 99.6 % / Redundancy: 5.6 % / B_iso Wilson estimate: 16 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.049 / R_pim(I) all: 0.023 / Net I/σ(I): 13.3
Reflection shell	Resolution: 1.22→1.29 Å / R_merge(I) obs: 1.036 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10919 / CC_1/2: 0.623 / R_pim(I) all: 0.481 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6F4R

6f4r

Resolution: 1.22→39.234 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1544	3767	5.01 %	RANDOM
R_work	0.1413	-	-	-
obs	0.1419	75238	99.51 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / B_sol: 54.1 Å² / k_sol: 0.41 e/Å³

Displacement parameters

B_iso mean: 26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.88 Å²	0 Å²	0 Å²
2-	-	-1.27 Å²	0 Å²
3-	-	-	5.14 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.16 Å	0.15 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	-	0.19 Å

Refinement step

Cycle: LAST / Resolution: 1.22→39.234 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1925	0	37	338	2300

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	2288
X-RAY DIFFRACTION	f_angle_d	1.511	3147
X-RAY DIFFRACTION	f_dihedral_angle_d	16.002	868
X-RAY DIFFRACTION	f_chiral_restr	0.106	323
X-RAY DIFFRACTION	f_plane_restr	0.012	427

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.22-1.2355	0.3613	130	0.3178	2614	X-RAY DIFFRACTION	100
1.2355-1.2517	0.313	122	0.2872	2656	X-RAY DIFFRACTION	100
1.2517-1.2689	0.246	119	0.2711	2639	X-RAY DIFFRACTION	100
1.2689-1.287	0.2753	140	0.2389	2622	X-RAY DIFFRACTION	100
1.287-1.3062	0.239	150	0.2253	2602	X-RAY DIFFRACTION	100
1.3062-1.3266	0.2269	133	0.2183	2672	X-RAY DIFFRACTION	100
1.3266-1.3484	0.2328	147	0.1991	2582	X-RAY DIFFRACTION	100
1.3484-1.3716	0.2122	141	0.1884	2644	X-RAY DIFFRACTION	100
1.3716-1.3966	0.1826	130	0.1759	2640	X-RAY DIFFRACTION	100
1.3966-1.4234	0.1702	135	0.1652	2622	X-RAY DIFFRACTION	100
1.4234-1.4525	0.1704	137	0.1627	2674	X-RAY DIFFRACTION	100
1.4525-1.4841	0.1743	130	0.1541	2623	X-RAY DIFFRACTION	100
1.4841-1.5186	0.1724	155	0.1476	2624	X-RAY DIFFRACTION	100
1.5186-1.5566	0.1743	123	0.145	2650	X-RAY DIFFRACTION	100
1.5566-1.5986	0.1749	154	0.1387	2647	X-RAY DIFFRACTION	100
1.5986-1.6457	0.1395	152	0.1331	2625	X-RAY DIFFRACTION	100
1.6457-1.6988	0.1428	142	0.1289	2648	X-RAY DIFFRACTION	100
1.6988-1.7595	0.1259	148	0.1298	2642	X-RAY DIFFRACTION	100
1.7595-1.83	0.1433	136	0.1273	2665	X-RAY DIFFRACTION	100
1.83-1.9133	0.1319	139	0.1283	2639	X-RAY DIFFRACTION	100
1.9133-2.0141	0.1273	138	0.1211	2645	X-RAY DIFFRACTION	99
2.0141-2.1403	0.1293	156	0.1207	2646	X-RAY DIFFRACTION	99
2.1403-2.3055	0.1458	143	0.1227	2627	X-RAY DIFFRACTION	98
2.3055-2.5375	0.1487	132	0.1267	2656	X-RAY DIFFRACTION	98
2.5375-2.9046	0.1606	125	0.1328	2702	X-RAY DIFFRACTION	99
2.9046-3.6591	0.1451	154	0.1286	2673	X-RAY DIFFRACTION	98
3.6591-39.2545	0.1503	156	0.146	2792	X-RAY DIFFRACTION	97

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	0.4195	-0.3304	-0.3308	0.2723	-0.0506	0.5219	0.0001	0.0188	0.2697	0.075	0.0879	0.2285	-0.1933	-0.2765	0.0497	0.1552	0.0482	0.0399	0.2243	0.0411	0.2383	-24.8699	21.783	-19.8526
2	0.2642	0.2045	-0.0991	0.1434	-0.0591	0.4383	-0.0544	-0.1623	0.1388	0.1944	0.1374	-0.0943	-0.1762	-0.0466	0.0021	0.2541	0.0358	0.0051	0.2222	-0.0311	0.1642	-8.5664	10.6131	-3.2113
3	0.9821	-0.3186	0.3583	0.5504	0.2951	0.3374	0.0705	0.2469	0.0501	-0.1884	-0.1333	-0.0692	0.0116	0.1786	0	0.2006	0.0284	0.0314	0.2057	0.0237	0.1781	3.297	4.4061	-22.2311
4	0.3439	-0.723	0.0377	0.8651	-0.5602	0.9791	0.0013	0.1643	0.1272	0.0695	-0.097	-0.2016	-0.0258	0.211	-0.0003	0.1413	-0.0108	0.0008	0.1597	0.0252	0.1882	4.6951	7.5956	-14.6053
5	0.31	-0.0706	-0.1504	0.4544	-0.099	0.06	-0.0697	-0.1116	-0.287	0.1203	0.1143	0.2531	0.0986	-0.1576	0.0036	0.187	-0.0144	0.0215	0.1991	0.0453	0.2404	-19.4347	4.6155	-13.0458
6	0.051	-0.11	0.0344	0.0883	-0.0594	0.0476	0.0483	0.0098	-0.0605	0.0045	0.0306	0.0677	0.0195	0.0426	0.0001	0.1456	0.0042	-0.0081	0.1306	-0.0036	0.1753	-9.3228	6.8672	-17.1222
7	0.2888	-0.1406	-0.32	0.3302	-0.2616	0.5279	0.0564	0.0925	-0.1081	-0.0127	0.0154	-0.0778	0.0462	0.0824	-0	0.1407	-0.0106	-0.0143	0.138	-0.006	0.1405	-6.2637	13.2785	-25.9522
8	0.2061	-0.1385	-0.1783	0.2626	-0.2587	0.3197	0.0214	-0.025	0.008	0.0921	0.0638	0.0452	-0.0557	-0.0203	0.0007	0.1331	0.0026	0.005	0.1169	0.0018	0.1126	-9.9543	18.6101	-20.0712
9	0.5606	-0.0282	-0.5836	0.465	-0.5356	0.8189	-0.063	0.183	-0.1039	-0.2564	0.01	-0.0042	0.0356	-0.0742	0.0001	0.1887	-0.0129	0.0057	0.1773	-0.0326	0.139	-7.7077	14.3188	-38.0593
10	0.1397	0.0364	-0.2377	0.4112	0.1831	0.1588	0.1472	0.1263	0.1147	-0.0453	-0.0233	-0.0833	-0.2363	0.0253	0.0019	0.1989	0.0134	0.0489	0.1918	0.0141	0.1465	-2.1117	24.7022	-39.1846
11	0.4325	-0.1619	-0.2342	0.2742	-0.3195	0.3238	0.0113	0.0017	0.0796	0.0584	0.0699	0.0946	-0.1045	-0.1064	0.0033	0.142	0.0044	0.0067	0.1331	0.0018	0.1414	-14.4111	19.1237	-23.0778
12	0.1684	-0.2864	-0.2181	0.4332	-0.6402	0.7006	0.0129	0.023	-0.0516	0.0373	0.0456	0.0298	-0.0416	-0.0341	0.0007	0.1354	-0.0071	-0.0097	0.1282	-0.0019	0.1356	-10.4638	13.2728	-19.5847

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 182:211)
2	X-RAY DIFFRACTION	2	(chain A and resid 212:230)
3	X-RAY DIFFRACTION	3	(chain A and resid 231:254)
4	X-RAY DIFFRACTION	4	(chain A and resid 255:277)
5	X-RAY DIFFRACTION	5	(chain A and resid 278:305)
6	X-RAY DIFFRACTION	6	(chain A and resid 306:312)
7	X-RAY DIFFRACTION	7	(chain A and resid 313:325)
8	X-RAY DIFFRACTION	8	(chain A and resid 326:341)
9	X-RAY DIFFRACTION	9	(chain A and resid 342:365)
10	X-RAY DIFFRACTION	10	(chain A and resid 366:381)
11	X-RAY DIFFRACTION	11	(chain A and resid 382:399)
12	X-RAY DIFFRACTION	12	(chain A and resid 400:416)

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Protein / Protein/peptide , 2 types, 2 molecules AB

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Non-polymers , 5 types, 344 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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