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- PDB-6f4s: Human JMJD5 (N308C) in complex with Mn(II), 2OG and RCCD1 (139-14... -

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Basic information

Entry
Database: PDB / ID: 6f4s
TitleHuman JMJD5 (N308C) in complex with Mn(II), 2OG and RCCD1 (139-143) (complex-4)
Components
  • JmjC domain-containing protein 5
  • RCC1 domain-containing protein 1
KeywordsOXIDOREDUCTASE / 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 / : / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / : / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromatin organization / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / : / KDM8-like, N-terminal ARM repeats / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cupin-like domain 8 / Cupin-like domain ...: / : / KDM8-like, N-terminal ARM repeats / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cupin-like domain 8 / Cupin-like domain / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / RCC1 domain-containing protein 1 / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.461 Å
AuthorsChowdhury, R. / Islam, M.S. / Schofield, C.J.
CitationJournal: 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
DepositionNov 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
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_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_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.pdbx_dist_value / _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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JmjC domain-containing protein 5
B: RCC1 domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5266
Polymers30,1112
Non-polymers4154
Water6,161342
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-9 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.321, 65.607, 77.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein JmjC domain-containing protein 5 / LYSINE-SPECIFIC DEMETHYLASE 8 / JUMONJI DOMAIN-CONTAINING PROTEIN 5


Mass: 29527.264 Da / Num. of mol.: 1 / Mutation: C217A, C232A, N308C
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN 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 / Source method: obtained synthetically / Details: FRAGMENT: 139-143 / Source: (synth.) Homo sapiens (human) / References: UniProt: A6NED2

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Non-polymers , 5 types, 346 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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 29 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2017 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.46→33.43 Å / Num. obs: 44375 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.05 / Net I/σ(I): 17
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 7 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 2 / Num. unique obs: 2928 / CC1/2: 0.602 / Rpim(I) all: 0.602 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000706Edata reduction
HKL-2000706Edata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F4R

6f4r


Resolution: 1.461→33.426 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.152 2188 4.94 %RANDOM
Rwork0.1367 ---
obs0.1375 44307 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 62.4 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å20 Å20 Å2
2--0.34 Å20 Å2
3---2.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.3 Å
Refinement stepCycle: LAST / Resolution: 1.461→33.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 25 342 2319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082440
X-RAY DIFFRACTIONf_angle_d0.9623364
X-RAY DIFFRACTIONf_dihedral_angle_d15.403934
X-RAY DIFFRACTIONf_chiral_restr0.085336
X-RAY DIFFRACTIONf_plane_restr0.007462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4613-1.49310.22621460.23182572X-RAY DIFFRACTION99
1.4931-1.52780.19861010.21032618X-RAY DIFFRACTION100
1.5278-1.5660.23121380.20072562X-RAY DIFFRACTION100
1.566-1.60840.20421600.18182595X-RAY DIFFRACTION100
1.6084-1.65570.20661300.16932595X-RAY DIFFRACTION100
1.6557-1.70910.17031450.1592599X-RAY DIFFRACTION100
1.7091-1.77020.16951430.14472611X-RAY DIFFRACTION100
1.7702-1.84110.17161350.13542615X-RAY DIFFRACTION100
1.8411-1.92490.13381320.13152610X-RAY DIFFRACTION100
1.9249-2.02640.13871190.11742630X-RAY DIFFRACTION100
2.0264-2.15330.13541410.11382640X-RAY DIFFRACTION100
2.1533-2.31950.11961370.10932644X-RAY DIFFRACTION100
2.3195-2.55290.14141380.11552648X-RAY DIFFRACTION100
2.5529-2.92210.15631370.12282669X-RAY DIFFRACTION100
2.9221-3.68080.13721460.11962692X-RAY DIFFRACTION100
3.6808-33.43450.14531400.15012819X-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)
10.8805-0.1679-0.4991.57170.54881.57030.00570.01620.22860.0730.08540.2724-0.2935-0.3660.07910.11650.05410.02950.17510.03620.1884-25.04122.3715-19.5715
22.4875-0.75270.80871.9717-0.4891.9064-0.1584-0.33540.26610.39880.1991-0.1509-0.3153-0.04450.00680.25180.03090.01140.2076-0.02760.1422-8.272610.3833-2.6835
30.9336-0.62960.54352.0521-1.13121.48480.0960.23830.0492-0.2901-0.1876-0.1440.11360.21120.0550.17020.02810.03130.17790.02160.15813.29034.4737-22.1839
41.3081-0.38720.122.3911-0.63921.83290.02810.07330.08030.0678-0.12-0.4189-0.04340.3691-0.02830.0997-0.00880.00460.14390.02250.17675.77797.7153-14.4776
52.095-0.84760.08581.7649-0.64920.669-0.0477-0.0115-0.54310.0130.12420.39670.1285-0.2378-0.08510.1648-0.02380.01640.17740.03070.2329-19.95863.8374-13.7133
63.04790.52570.10691.9183-0.03541.0875-0.03420.1138-0.1907-0.04340.09680.08220.0196-0.01340.01340.10510.0065-0.00180.0914-0.00540.1172-8.45787.51-16.5127
71.5806-0.25720.25560.835-0.58261.74680.00280.145-0.09660.01340.0299-0.08320.02080.11250.03420.09530.0013-0.00590.0826-0.01130.0918-6.35913.4274-25.5823
80.70880.0398-0.03551.0594-0.61161.52480.0079-0.04860.00530.10890.02570.0283-0.0998-0.00250.0350.0970.00940.00510.0866-0.00750.09-10.038618.7642-19.7509
91.90890.0441-0.66132.1523-0.64142.3267-0.04920.2676-0.3192-0.2968-0.02230.05660.2941-0.0827-0.00320.1771-0.01470.00340.1418-0.02880.1278-8.013115.1023-37.4026
100.7443-0.248-1.07561.37210.89092.50580.17390.27440.0594-0.1631-0.0404-0.113-0.25540.0575-0.02320.17160.00080.04040.15320.01070.1209-2.151124.8335-38.8253
111.25480.235-0.29071.2695-0.4671.53480.0025-0.00020.0730.05690.05680.1055-0.1249-0.09110.01240.09290.02630.00340.08650.00010.1042-14.494419.296-22.7439
120.742-0.1589-0.491.0999-1.08611.725-0.00910.0447-0.07140.03620.05210.02150.0333-0.06660.02220.10070.0082-0.00730.0845-0.00890.0943-10.711613.0317-19.6228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 182:211)
2X-RAY DIFFRACTION2(chain A and resid 212:230)
3X-RAY DIFFRACTION3(chain A and resid 231:254)
4X-RAY DIFFRACTION4(chain A and resid 255:277)
5X-RAY DIFFRACTION5(chain A and resid 278:305)
6X-RAY DIFFRACTION6(chain A and resid 306:312)
7X-RAY DIFFRACTION7(chain A and resid 313:325)
8X-RAY DIFFRACTION8(chain A and resid 326:341)
9X-RAY DIFFRACTION9(chain A and resid 342:365)
10X-RAY DIFFRACTION10(chain A and resid 366:381)
11X-RAY DIFFRACTION11(chain A and resid 382:399)
12X-RAY DIFFRACTION12(chain A and resid 400:416)

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