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- PDB-6f4p: Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1) -

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Basic information

Entry
Database: PDB / ID: 6f4p
TitleHuman JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1)
Components
  • 40S ribosomal protein S6
  • JmjC domain-containing protein 5
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) / mammalian oogenesis stage / activation-induced cell death of T cells / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / Ribosomal scanning and start codon recognition / Translation initiation complex formation ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / mammalian oogenesis stage / activation-induced cell death of T cells / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Protein hydroxylation / TOR signaling / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / T cell proliferation involved in immune response / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / aminopeptidase activity / erythrocyte development / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nuclear events stimulated by ALK signaling in cancer / : / gastrulation / cytosolic ribosome / regulation of signal transduction by p53 class mediator / small-subunit processome / placenta development / circadian regulation of gene expression / protein destabilization / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / G2/M transition of mitotic cell cycle / p53 binding / glucose homeostasis / T cell differentiation in thymus / chromosome / cell body / ribosomal small subunit biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / fibroblast proliferation / SARS-CoV-2 modulates host translation machinery / endopeptidase activity / in utero embryonic development / cytoplasmic translation / structural constituent of ribosome / positive regulation of apoptotic process / translation / ribonucleoprotein complex / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / dendrite / chromatin binding / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / proteolysis / RNA binding / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / KDM8-like, N-terminal ARM repeats / Cupin-like domain 8 / Cupin-like domain / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Ribosomal protein S6, eukaryotic / Ribosomal protein S6/S6e/A/B/2, conserved site ...: / KDM8-like, N-terminal ARM repeats / Cupin-like domain 8 / Cupin-like domain / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Ribosomal protein S6, eukaryotic / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Small ribosomal subunit protein eS6 / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 29, 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

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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: 40S ribosomal protein S6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7095
Polymers31,3842
Non-polymers3243
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.283, 64.925, 78.037
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 / Jumonji domain-containing protein 5 / Lysine-specific demethylase 8


Mass: 29474.092 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 183-416
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 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 1910.385 Da / Num. of mol.: 1 / Fragment: UNP residues 129-144 / Source method: obtained synthetically / Details: FRAGMENT: 129-144 / Source: (synth.) Homo sapiens (human) / References: UniProt: P62753

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Non-polymers , 4 types, 332 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


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Bis-Tris pH 6.0, 26.4 % 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: Jan 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→32.46 Å / Num. obs: 44727 / % possible obs: 98.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.035 / Net I/σ(I): 19
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4347 / CC1/2: 0.634 / Rpim(I) all: 0.497 / % possible all: 97.7

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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: 6F4O

6f4o


Resolution: 1.45→32.46 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1682 2165 4.86 %Random
Rwork0.1463 ---
obs0.1473 44577 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 60.3 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å20 Å20 Å2
2---0.23 Å20 Å2
3---3.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.16 Å
Refinement stepCycle: LAST / Resolution: 1.45→32.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 19 329 2257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092299
X-RAY DIFFRACTIONf_angle_d1.0053169
X-RAY DIFFRACTIONf_dihedral_angle_d13.552860
X-RAY DIFFRACTIONf_chiral_restr0.087324
X-RAY DIFFRACTIONf_plane_restr0.008428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48380.27661490.27722728X-RAY DIFFRACTION98
1.4838-1.52090.25641470.23952735X-RAY DIFFRACTION98
1.5209-1.5620.27141520.21882766X-RAY DIFFRACTION98
1.562-1.6080.23761280.19672773X-RAY DIFFRACTION98
1.608-1.65980.19251220.17422815X-RAY DIFFRACTION98
1.6598-1.71920.19241510.16732764X-RAY DIFFRACTION99
1.7192-1.7880.18421420.15172807X-RAY DIFFRACTION99
1.788-1.86940.15581380.14262810X-RAY DIFFRACTION99
1.8694-1.96790.15691530.13262828X-RAY DIFFRACTION99
1.9679-2.09120.15221430.11882824X-RAY DIFFRACTION99
2.0912-2.25260.14321250.12742875X-RAY DIFFRACTION99
2.2526-2.47920.171420.12632867X-RAY DIFFRACTION100
2.4792-2.83780.13881600.1322864X-RAY DIFFRACTION100
2.8378-3.57460.13351570.12812910X-RAY DIFFRACTION100
3.5746-32.47060.18381560.15493046X-RAY DIFFRACTION100
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)
10.649-0.3896-0.07540.5881-0.17860.6781-0.0281-0.05550.21420.05350.11280.2294-0.2799-0.36230.08640.16440.06780.03330.25460.03530.2274-24.850422.4529-20.6559
20.21680.20290.0980.21440.10670.7011-0.1366-0.18020.0650.35260.2047-0.0526-0.1163-0.04950.00010.28180.05220.0080.2658-0.01840.184-8.436810.4684-3.2697
30.8449-0.37030.2240.72420.39170.38250.07380.25960.0536-0.2634-0.1427-0.11690.04710.09010.00010.21250.03820.03460.2010.04880.21792.96374.2589-21.424
40.5405-0.98210.04661.2747-0.68881.1544-0.01670.20440.02930.0487-0.1099-0.30240.02340.2346-0.04120.136-0.007-0.01570.13630.0390.21615.0427.8287-13.9283
50.3360.284-0.32230.6663-0.65770.3198-0.11950.026-0.35950.030.08090.26930.1506-0.2196-0.02870.2144-0.01730.0170.24810.04740.2799-19.20954.6584-12.7545
60.1685-0.2996-0.13830.26480.19620.09010.1275-0.0098-0.00480.03120.02320.1649-0.01560.09840.00050.15710.0112-0.01920.11970.00430.1659-8.90717.2352-16.8008
70.2412-0.1028-0.33380.4197-0.15310.57230.03840.147-0.1013-0.02510.0222-0.06650.09290.098900.1315-0.0059-0.01590.1244-0.00650.1349-6.397813.3364-25.7345
80.4259-0.2724-0.0460.412-0.11310.3059-0.0038-0.07750.01540.07920.05390.0374-0.0713-0.0083-00.1554-0.0004-0.00610.1428-0.0030.1387-9.74419.0998-20.1389
90.68090.0155-0.86220.4851-0.69291.1714-0.03520.2325-0.176-0.1987-0.0035-0.03250.1719-0.0361-0.00010.1823-0.01670.01040.1363-0.02890.1123-8.031714.4035-37.6983
100.24450.2436-0.13010.47360.29320.24380.21420.09890.1327-0.0126-0.006-0.1104-0.32810.09720.00150.19720.0210.05540.18790.01590.1516-2.217224.646-39.1006
110.6479-0.0195-0.1940.3978-0.40180.312-0.01630.04350.05310.04570.08870.1128-0.1174-0.06130.00110.14780.0160.00280.1393-0.00250.1381-14.56119.1766-22.9708
120.4876-0.3829-0.45980.6424-0.68140.7693-0.02870.0447-0.09810.04420.0816-0.01230.0092-0.0405-00.1421-0.0053-0.01040.1322-0.00130.1362-10.755213.0232-19.7345
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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