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- PDB-4nif: Heterodimeric structure of ERK2 and RSK1 -

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Basic information

Entry
Database: PDB / ID: 4nif
TitleHeterodimeric structure of ERK2 and RSK1
Components
  • Mitogen-activated protein kinase 1
  • Ribosomal protein S6 kinase alpha-1
KeywordsTRANSFERASE / Kinase domain / SIGNALING / Substrate kinase binding
Function / homology
Function and homology information


regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / ERKs are inactivated / cytosine metabolic process / response to epidermal growth factor / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / Regulation of the apoptosome activity / outer ear morphogenesis / regulation of cellular pH / negative regulation of TOR signaling / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / lung morphogenesis / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / regulation of cytoskeleton organization / Activation of the AP-1 family of transcription factors / face development / ERK/MAPK targets / progesterone receptor signaling pathway / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / pseudopodium / Recycling pathway of L1 / MAPK1 (ERK2) activation / Bergmann glial cell differentiation / negative regulation of cell differentiation / positive regulation of telomere capping / thyroid gland development / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Advanced glycosylation endproduct receptor signaling / steroid hormone receptor signaling pathway / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / MAP kinase activity / regulation of ossification / RHO GTPases Activate WASPs and WAVEs / mitogen-activated protein kinase / phosphatase binding / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Nuclear events stimulated by ALK signaling in cancer / Schwann cell development / Growth hormone receptor signaling / stress-activated MAPK cascade / lipopolysaccharide-mediated signaling pathway / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / cellular response to cadmium ion / NPAS4 regulates expression of target genes / ERK1 and ERK2 cascade / cellular response to amino acid starvation / myelination / protein serine/threonine/tyrosine kinase activity / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription / Signal transduction by L1 / caveola / long-term synaptic potentiation / Negative regulation of FGFR3 signaling / positive regulation of cell differentiation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR2 signaling / FCERI mediated MAPK activation / Negative regulation of FGFR4 signaling / FCGR3A-mediated phagocytosis / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
Similarity search - Function
Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Mitogen-activated protein (MAP) kinase, ERK1/2 / Protein kinase, C-terminal / Protein kinase C terminal domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. ...Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Mitogen-activated protein (MAP) kinase, ERK1/2 / Protein kinase, C-terminal / Protein kinase C terminal domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase 1 / Ribosomal protein S6 kinase alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGogl, G. / Remenyi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural assembly of the signaling competent ERK2-RSK1 heterodimeric protein kinase complex
Authors: Alexa, A. / Gogl, G. / Glatz, G. / Garai, A. / Zeke, A. / Varga, J. / Dudas, E. / Jeszenoi, N. / Bodor, A. / Hetenyi, C. / Remenyi, A.
History
DepositionNov 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: 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_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase alpha-1
B: Mitogen-activated protein kinase 1
D: Ribosomal protein S6 kinase alpha-1
E: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,51011
Polymers158,1634
Non-polymers1,3477
Water18,1231006
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-120 kcal/mol
Surface area56020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.490, 87.850, 116.540
Angle α, β, γ (deg.)90.00, 108.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein Ribosomal protein S6 kinase alpha-1 / S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase- ...S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase-activated protein kinase 1a / MAPK-activated protein kinase 1a / MAPKAP kinase 1a / MAPKAPK-1a / Ribosomal S6 kinase 1 / RSK-1


Mass: 37492.809 Da / Num. of mol.: 2 / Fragment: C-terminal kinase domain, UNP residues 411-735
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA1, MAPKAPK1A, RSK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15418, non-specific serine/threonine protein kinase
#2: Protein Mitogen-activated protein kinase 1 / MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform ...MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAP kinase 2 / MAPK 2


Mass: 41588.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28482, mitogen-activated protein kinase

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Non-polymers , 4 types, 1013 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 0.1M MES, 15% PEG4000, 0.125M (NH4)2SO4, 2% Benzamidine, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91961 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 24, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91961 Å / Relative weight: 1
ReflectionResolution: 2.15→60.63 Å / Num. all: 97610 / Num. obs: 97338 / % possible obs: 99.7 % / Observed criterion σ(F): 2.68 / Observed criterion σ(I): 2.68
Reflection shellResolution: 2.15→2.227 Å / % possible all: 99.85

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1439) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y9Q(for chain B,E), 2WNT(for chain A,D).

2y9q

2wnt


Resolution: 2.15→60.63 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 4859 4.99 %RANDOM
Rwork0.158 ---
obs0.1605 97289 99.76 %-
all-97610 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→60.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10503 0 79 1006 11588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710904
X-RAY DIFFRACTIONf_angle_d1.02814815
X-RAY DIFFRACTIONf_dihedral_angle_d14.784133
X-RAY DIFFRACTIONf_chiral_restr0.0411644
X-RAY DIFFRACTIONf_plane_restr0.0051905
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.17440.28451560.23443060100
2.1744-2.20.26111490.21323062100
2.2-2.22680.2451590.20593052100
2.2268-2.2550.27191750.19223053100
2.255-2.28470.23131690.19193069100
2.2847-2.3160.23751660.18763088100
2.316-2.34910.26541230.18413083100
2.3491-2.38410.25741710.18063053100
2.3841-2.42140.22771610.17753095100
2.4214-2.46110.21781610.16713085100
2.4611-2.50350.25661640.17353041100
2.5035-2.5490.21941570.16993080100
2.549-2.59810.25681540.17473094100
2.5981-2.65110.21211660.17313078100
2.6511-2.70870.23861570.16163072100
2.7087-2.77180.221620.16193069100
2.7718-2.84110.23391530.15883102100
2.8411-2.91790.22531930.16463048100
2.9179-3.00370.231670.16263047100
3.0037-3.10070.19641610.15943098100
3.1007-3.21150.18521650.15723063100
3.2115-3.34010.2171480.15313115100
3.3401-3.49210.18611540.15413097100
3.4921-3.67620.18511610.1453092100
3.6762-3.90650.20671610.13693119100
3.9065-4.2080.17191660.13633066100
4.208-4.63130.17831840.1254307399
4.6313-5.30120.18391650.14133098100
5.3012-6.67760.21431610.17043126100
6.6776-60.65770.18971700.1617315298
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)
12.1401-0.5188-0.31694.04640.63184.6752-0.49040.01650.34460.35140.2681-0.1147-1.39740.0060.20950.62320.0316-0.11370.343-0.05620.3118-22.482243.616-16.3289
22.29860.2343-1.09152.38390.47553.8943-0.2523-0.05410.3828-0.12320.0770.4005-0.3807-0.45770.06710.2360.112-0.07840.308-0.04760.2902-33.580735.0662-7.286
36.8156-4.7324-1.44067.37592.8284.8833-0.1372-0.19520.1502-0.03270.06620.2292-0.1177-0.1680.04350.1667-0.00140.02610.28720.00460.1536-30.252827.5768-5.9662
44.5309-3.5461-3.09393.80483.89654.0355-0.2512-0.51950.20230.48290.25250.010.0348-0.14020.00170.27450.10060.02860.3441-0.02010.2351-29.471925.03045.8836
56.66481.1033-0.33613.83530.98673.59730.117-1.089-0.07261.1283-0.15870.05060.2005-0.16430.02340.61560.17340.07370.56350.00490.3638-32.285731.372317.0005
64.1318-0.6638-1.05653.57560.69192.7058-0.307-0.57950.5480.3127-0.06980.7131-0.2127-0.38020.30320.39970.13950.05410.4727-0.10660.4514-37.559835.56319.3878
72.4764-3.7120.30936.6790.64973.27490.0988-0.5525-0.52430.73080.1012-0.39130.20280.218-0.15350.2859-0.0369-0.12560.2718-0.05520.72339.532922.47195.0642
81.95770.3118-0.33782.2234-0.30171.01350.0007-0.26220.05760.4713-0.0009-0.0926-0.14680.0035-0.00920.27510.0451-0.08470.2303-0.01820.2484-6.27069.57686.1202
97.98340.11-0.61116.0319-1.29923.5936-0.16680.8208-0.3572-0.681-0.06090.67830.5317-0.17810.23260.31890.0091-0.11690.24980.00340.2633-3.89270.7704-6.0702
104.2839-0.53190.33611.9957-0.25833.83020.01090.7921-0.3083-0.4061-0.0543-0.05890.2382-0.00120.05720.23980.00110.00170.3065-0.05290.2706-5.82139.4027-20.6806
112.3490.2728-0.48442.395-0.60281.2697-0.07390.2114-0.1474-0.08930.0072-0.41960.01350.03760.04820.16360.0402-0.04930.2178-0.04760.34792.22025.0465-8.1591
125.40531.40961.06425.7421-1.27552.50520.50820.1618-0.8694-0.52010.38690.0851.243-0.1969-0.82070.5132-0.1074-0.14930.3740.02540.3806-28.17014.669-26.3466
134.0539-0.61420.01225.58291.18711.38520.07810.1494-0.1737-0.2728-0.0285-0.04760.1517-0.3048-0.06330.2276-0.0913-0.04870.30190.020.2249-29.846217.913-28.3038
143.63310.27980.3541.7089-0.12261.2751-0.0187-0.2179-0.18910.11630.17050.28830.2867-0.342-0.04460.2875-0.10590.02790.37740.09570.2388-43.547414.4341-23.7326
154.98733.8847-0.79629.3229-1.86833.9876-0.0579-0.1497-0.0070.12870.080.23780.0245-0.3811-0.02990.15180.0198-0.00010.30740.01770.1722-41.197423.451-27.1753
164.67324.6309-1.60644.5592-1.41841.6932-0.33090.25040.2709-0.44350.63560.71320.0762-0.6271-0.10620.2809-0.0515-0.02270.42080.1280.349-50.469725.9335-34.7662
174.1019-1.0356-3.11685.83590.60014.43730.17961.565-0.2332-1.8395-0.13980.37020.2651-0.8672-0.03270.9116-0.1761-0.20080.98210.09230.4724-57.078414.7164-46.0365
185.4663-0.01230.14514.91875.53846.25360.02350.51580.7502-1.10480.00341.6024-0.667-1.34860.02630.4934-0.0116-0.15810.82980.31650.8131-63.966722.4556-33.9628
193.95750.236-0.74884.98180.91564.2584-0.10130.0440.219-0.07080.28970.82780.4247-0.7467-0.16040.3042-0.0715-0.01150.56960.14240.5153-57.98315.3143-29.5775
207.26356.0111-2.33889.635-5.76247.5811-0.13330.53940.1334-0.34390.32770.2042-0.3452-0.3977-0.09650.62550.0360.12080.2679-0.06040.3283-27.350328.4626-65.8809
211.394-0.3165-0.2532.428-0.15091.05610.05590.149-0.1014-0.27350.01480.31750.1016-0.2044-0.07720.3693-0.0442-0.03620.24150.02380.1839-36.848141.4692-53.917
225.1193-1.6935-3.05123.839-1.91046.02510.1274-0.44120.77590.9953-0.024-0.4271-0.25810.5621-0.11370.38360.0182-0.06740.2084-0.00520.2617-25.969150.3182-48.6726
233.57741.5999-0.58210.7933-0.87956.37830.1266-0.24380.1240.1946-0.1478-0.2435-0.20320.32780.02630.2934-0.0163-0.00660.18910.01120.2192-18.491139.5854-40.3293
243.5733-2.828-1.1712.96030.15442.0390.3496-1.33660.79860.6668-0.90250.3115-0.9637-0.8580.71090.6963-0.166-0.14670.9821-0.23790.735-5.376948.3042-32.6128
252.4202-0.804-0.74042.2237-0.0811.34440.1-0.12170.0976-0.2028-0.0223-0.2569-0.09420.168-0.05820.3514-0.06110.04430.19690.010.1921-20.571346.1369-52.5001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 413 through 456 )
2X-RAY DIFFRACTION2chain 'A' and (resid 457 through 529 )
3X-RAY DIFFRACTION3chain 'A' and (resid 530 through 582 )
4X-RAY DIFFRACTION4chain 'A' and (resid 583 through 609 )
5X-RAY DIFFRACTION5chain 'A' and (resid 610 through 665 )
6X-RAY DIFFRACTION6chain 'A' and (resid 666 through 706 )
7X-RAY DIFFRACTION7chain 'A' and (resid 707 through 728 )
8X-RAY DIFFRACTION8chain 'B' and (resid 9 through 162 )
9X-RAY DIFFRACTION9chain 'B' and (resid 163 through 183 )
10X-RAY DIFFRACTION10chain 'B' and (resid 184 through 266 )
11X-RAY DIFFRACTION11chain 'B' and (resid 267 through 360 )
12X-RAY DIFFRACTION12chain 'D' and (resid 413 through 441 )
13X-RAY DIFFRACTION13chain 'D' and (resid 442 through 466 )
14X-RAY DIFFRACTION14chain 'D' and (resid 467 through 529 )
15X-RAY DIFFRACTION15chain 'D' and (resid 530 through 582 )
16X-RAY DIFFRACTION16chain 'D' and (resid 583 through 609 )
17X-RAY DIFFRACTION17chain 'D' and (resid 610 through 631 )
18X-RAY DIFFRACTION18chain 'D' and (resid 632 through 665 )
19X-RAY DIFFRACTION19chain 'D' and (resid 666 through 706 )
20X-RAY DIFFRACTION20chain 'D' and (resid 707 through 728 )
21X-RAY DIFFRACTION21chain 'E' and (resid 10 through 162 )
22X-RAY DIFFRACTION22chain 'E' and (resid 163 through 183 )
23X-RAY DIFFRACTION23chain 'E' and (resid 184 through 244 )
24X-RAY DIFFRACTION24chain 'E' and (resid 245 through 266 )
25X-RAY DIFFRACTION25chain 'E' and (resid 267 through 360 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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