[English] 日本語
Yorodumi
- PDB-6no7: Crystal Structure of the full-length wild-type PKA RIa Holoenzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6no7
TitleCrystal Structure of the full-length wild-type PKA RIa Holoenzyme
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase type I-alpha regulatory subunit
KeywordsSIGNALING PROTEIN / PKA / RIa holoenzyme / ATP-dependent
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / sperm head-tail coupling apparatus / ROBO receptors bind AKAP5 / channel activator activity / HDL assembly / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / sperm head-tail coupling apparatus / ROBO receptors bind AKAP5 / channel activator activity / HDL assembly / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly / Rap1 signalling / intracellular potassium ion homeostasis / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / Loss of phosphorylation of MECP2 at T308 / cardiac muscle cell proliferation / cAMP-dependent protein kinase activity / sarcomere organization / CREB1 phosphorylation through the activation of Adenylate Cyclase / protein localization to lipid droplet / PKA activation / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of interleukin-2 production / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / Triglyceride catabolism / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / negative regulation of activated T cell proliferation / mesoderm formation / cAMP/PKA signal transduction / RET signaling / Regulation of MECP2 expression and activity / sperm flagellum / Interleukin-3, Interleukin-5 and GM-CSF signaling / PKA activation in glucagon signalling / plasma membrane raft / immunological synapse / DARPP-32 events / axoneme / regulation of cardiac conduction / regulation of macroautophagy / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / postsynaptic modulation of chemical synaptic transmission / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / Hedgehog 'off' state / cAMP binding / positive regulation of phagocytosis / Ion homeostasis / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / cellular response to epinephrine stimulus / sperm midpiece / multivesicular body / calcium channel complex / Mitochondrial protein degradation / positive regulation of gluconeogenesis / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / CD209 (DC-SIGN) signaling / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / FCGR3A-mediated IL10 synthesis / positive regulation of calcium-mediated signaling / regulation of heart rate / protein export from nucleus / acrosomal vesicle / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / Regulation of insulin secretion / neural tube closure / Degradation of GLI1 by the proteasome / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / Jelly Rolls / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Jelly Rolls / 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 / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / cAMP-dependent protein kinase type I-alpha regulatory subunit / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsLu, T. / Wu, J. / Taylor, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM34921 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Two PKA RI alpha holoenzyme states define ATP as an isoform-specific orthosteric inhibitor that competes with the allosteric activator, cAMP.
Authors: Lu, T.W. / Wu, J. / Aoto, P.C. / Weng, J.H. / Ahuja, L.G. / Sun, N. / Cheng, C.Y. / Zhang, P. / Taylor, S.S.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 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
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.ptnr1_label_seq_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_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.ptnr3_label_seq_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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
C: cAMP-dependent protein kinase catalytic subunit alpha
D: cAMP-dependent protein kinase type I-alpha regulatory subunit
E: cAMP-dependent protein kinase catalytic subunit alpha
F: cAMP-dependent protein kinase type I-alpha regulatory subunit
G: cAMP-dependent protein kinase catalytic subunit alpha
H: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,93114
Polymers334,8208
Non-polymers1,1126
Water00
1
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
C: cAMP-dependent protein kinase catalytic subunit alpha
D: cAMP-dependent protein kinase type I-alpha regulatory subunit


Theoretical massNumber of molelcules
Total (without water)167,4104
Polymers167,4104
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: cAMP-dependent protein kinase catalytic subunit alpha
F: cAMP-dependent protein kinase type I-alpha regulatory subunit
G: cAMP-dependent protein kinase catalytic subunit alpha
H: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,52210
Polymers167,4104
Non-polymers1,1126
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.778, 184.811, 183.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 40757.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein
cAMP-dependent protein kinase type I-alpha regulatory subunit


Mass: 42947.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PRKAR1A / Production host: Escherichia coli (E. coli) / References: UniProt: P00514
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: mixing 1 ul of the protein solution (7.5 mg/ml) and 1 ul of the reservoir solution (100 mM imidazole/MES pH=7.0, 100 mM NPS, 16.8% v/v Ethylene glycol, 8.4 % w/v PEG 8000).

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2017
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.55→50 Å / Num. obs: 58193 / % possible obs: 87 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 7.6
Reflection shellResolution: 3.55→3.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2567 / % possible all: 80.7

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCS

2qcs


Resolution: 3.55→47.632 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 37.27 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 2816 5.57 %Random selection
Rwork0.2558 ---
obs0.2591 50530 87.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.55→47.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20062 0 66 0 20128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00520577
X-RAY DIFFRACTIONf_angle_d1.21327821
X-RAY DIFFRACTIONf_dihedral_angle_d11.42912299
X-RAY DIFFRACTIONf_chiral_restr0.0622978
X-RAY DIFFRACTIONf_plane_restr0.0063587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5501-3.61830.35661120.3592228X-RAY DIFFRACTION70
3.6183-3.69220.39191390.34752278X-RAY DIFFRACTION71
3.6922-3.77240.3011170.34952339X-RAY DIFFRACTION73
3.7724-3.86010.32891140.32422350X-RAY DIFFRACTION74
3.8601-3.95650.35051260.30942353X-RAY DIFFRACTION74
3.9565-4.06340.28161380.28082451X-RAY DIFFRACTION76
4.0634-4.18290.32791310.29172473X-RAY DIFFRACTION77
4.1829-4.31780.27091370.27262488X-RAY DIFFRACTION78
4.3178-4.47190.27461290.25932560X-RAY DIFFRACTION80
4.4719-4.65070.25911500.25422616X-RAY DIFFRACTION82
4.6507-4.86210.27951560.25112703X-RAY DIFFRACTION85
4.8621-5.1180.26671520.24962837X-RAY DIFFRACTION88
5.118-5.4380.28961480.26112905X-RAY DIFFRACTION90
5.438-5.85680.33541500.28333028X-RAY DIFFRACTION94
5.8568-6.44430.30041620.2723059X-RAY DIFFRACTION94
6.4443-7.37230.26391640.2313075X-RAY DIFFRACTION94
7.3723-9.27120.19481530.21413110X-RAY DIFFRACTION94
9.2712-41.54140.22091620.22833126X-RAY DIFFRACTION91
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)
10.06210.1884-0.13561.0805-0.32641.19770.01150.62030.70590.13550.4723-0.697-0.81760.2165-0.46391.3385-0.11280.59192.0861-0.1681.73633.693742.725218.7044
20.9608-0.7388-0.04241.18110.20562.0645-0.50331.1077-0.1022-0.17480.3798-0.9269-0.22221.0589-0.06440.5559-0.18650.51561.2025-0.40791.942531.709929.611119.2519
33.76571.36651.32654.49071.43052.1391-0.1840.2896-0.36710.8548-0.05260.49280.2040.03940.40020.6501-0.05510.01130.9274-0.05991.30277.494247.160541.6428
42.03060.3087-1.89190.9361-0.48831.7342-0.0419-0.24030.71840.517-0.2957-1.0529-0.40370.30610.34371.23880.215-0.21642.88130.40831.557452.2352-19.204753.9217
50.242-0.3231-0.09050.33880.07810.79130.59-0.393-0.1723-0.1068-0.2047-0.8907-0.00310.7126-0.14650.6957-0.2479-0.4061.86060.15842.495456.0935-16.297644.9629
61.5674-0.106-0.13070.3425-0.47590.7851-0.5604-0.5194-0.9747-0.2271-0.8311-1.40920.93910.9058-0.45020.08860.269-0.10522.03910.92612.401843.8383-34.874735.5541
70.73070.65880.9345.04670.99451.20570.2263-0.31-0.21370.5763-0.39741.47270.3115-0.49770.26781.9668-0.5376-0.46960.9807-0.27493.307753.6216-0.362942.9782
80.7257-0.15491.01260.7858-1.00812.36060.0846-1.2575-0.37650.6835-0.1572-0.9201-0.14040.45410.07151.09940.2943-0.26571.3799-0.18011.396433.604-11.444429.6287
91.62670.5105-0.65771.5415-0.46820.9004-0.54930.5521-0.0696-0.4707-0.0532-0.85330.00950.7914-0.05950.07650.0535-0.09411.3833-0.01251.5530.6799-12.310817.0488
102.9703-0.38390.68022.1675-0.5293.9821-0.1892-0.87410.1878-0.4063-0.0339-0.30370.1342-0.76480.04670.53630.0785-0.12161.15010.17971.32357.3796-34.451937.0702
114.44190.2261-3.80260.0025-0.11723.3359-0.0393-0.28681.3148-0.129-0.18840.4598-1.0357-0.45330.07911.44150.60990.082.59840.16842.0229-23.41618.1173-20.7967
120.7814-0.1139-0.4440.29480.44321.24350.73940.34850.2946-0.1513-0.07670.414-0.1318-0.3889-0.31241.09430.3093-0.23742.289-0.27641.9954-27.21824.9021-12.1781
131.87070.21720.53410.89720.44231.09380.45961.9908-0.3689-0.5521-0.79850.03960.1057-2.2008-0.09610.58220.2161-0.1593.3948-0.38420.9908-15.1829-15.4251-17.5555
142.47430.19980.7091.54530.21640.2216-0.1858-0.08350.6379-0.4445-0.2899-0.514-0.41520.52540.00431.41190.4875-0.29242.3954-0.27142.2359-24.59416.0833-1.2075
152.1226-0.13792.92090.2294-0.18324.22820.02730.62560.7997-0.7449-0.46210.1045-0.8680.34320.62391.14510.176-0.44831.3553-0.26551.4127-4.3298-1.22281.5487
162.9673-0.2579-0.73331.56190.89391.5791-0.3814-0.7915-0.17740.0627-0.29760.6638-0.0934-0.75850.37320.51090.1599-0.03381.46220.0230.9575-1.7357-10.093410.6567
172.70180.35821.71593.9491-0.88954.8338-0.2450.2057-0.0331-0.0823-0.0566-0.20710.15340.39490.22780.68130.06880.08521.4898-0.10890.955521.1528-14.0799-18.5575
183.93150.142.43621.21650.12852.3009-0.3151-0.2581-0.81160.2504-0.3233-0.02131.0044-0.17730.60611.14640.01020.261.81250.3991.5813-10.7769-8.854262.2288
191.5020.08850.09921.30161.35221.57950.4944-1.0173-1.4220.3322-0.35590.2631-0.0509-1.13860.10330.8208-0.140.18561.4263-0.01731.7424-15.3499-5.321453.4958
202.6876-0.0076-0.61492.4451-0.10222.09910.0937-1.07380.41250.349-0.3029-0.070.0543-0.75860.14950.5502-0.02580.14191.5007-0.07520.8606-3.033614.284658.1856
210.9749-1.7949-0.59673.50720.81820.7372-0.07480.005-0.27620.5117-0.35880.05990.5608-0.5094-0.0041.6738-0.3580.47420.7364-0.95512.3286-13.7155-16.353741.784
222.54980.0945-0.74521.7646-0.61561.7510.1068-0.8301-1.0239-0.0174-0.36190.37140.2095-0.70830.11310.5777-0.0814-0.18811.1086-0.39111.50976.87070.754437.844
233.05920.82350.6891.88710.1482.5469-0.92761.7990.26950.06880.23570.82750.2572-0.55620.13190.261-0.22850.06621.3351-0.26560.93749.04910.016628.5348
243.63890.6361-1.1491.7345-0.1632.537-0.44720.6175-0.08250.0126-0.2137-0.1988-0.06230.20170.64160.6263-0.1286-0.27191.4521-0.13091.251933.575413.533456.8632
257.2069-4.1012-3.16942.33911.96792.2077-0.42231.04590.7503-0.9726-0.1453-1.1207-0.30331.17980.24751.2698-0.31490.59221.90510.09343.302251.478867.797629.6437
260.0254-0.0418-0.15230.1328-0.06811.30911.00350.76830.9473-0.1835-0.1512-0.8331-0.45041.0846-0.49881.1364-0.49790.28212.348-0.01472.243555.850858.831825.3147
271.72170.6011-0.01410.84680.33011.17730.3356-0.32950.64810.09870.8158-1.05410.23440.81220.12830.1376-0.3182-0.12281.1316-0.89162.851544.25748.129842.7172
288.9663-2.25070.83551.6795-0.8670.4832-0.20290.65180.2901-0.4801-0.13160.1629-0.4641-0.22380.0552.0808-0.32290.28472.3695-0.09611.967554.196258.31089.4156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 93 through 118 )
2X-RAY DIFFRACTION2chain 'D' and (resid 119 through 250 )
3X-RAY DIFFRACTION3chain 'D' and (resid 251 through 372 )
4X-RAY DIFFRACTION4chain 'E' and (resid 15 through 49 )
5X-RAY DIFFRACTION5chain 'E' and (resid 58 through 128 )
6X-RAY DIFFRACTION6chain 'E' and (resid 129 through 318 )
7X-RAY DIFFRACTION7chain 'E' and (resid 336 through 350 )
8X-RAY DIFFRACTION8chain 'F' and (resid 93 through 118 )
9X-RAY DIFFRACTION9chain 'F' and (resid 119 through 250)
10X-RAY DIFFRACTION10chain 'F' and (resid 251 through 372 )
11X-RAY DIFFRACTION11chain 'G' and (resid 15 through 49 )
12X-RAY DIFFRACTION12chain 'G' and (resid 58 through 128 )
13X-RAY DIFFRACTION13chain 'G' and (resid 129 through 318 )
14X-RAY DIFFRACTION14chain 'G' and (resid 336 through 350 )
15X-RAY DIFFRACTION15chain 'H' and (resid 93 through 118 )
16X-RAY DIFFRACTION16chain 'H' and (resid 119 through 250 )
17X-RAY DIFFRACTION17chain 'H' and (resid 251 through 372 )
18X-RAY DIFFRACTION18chain 'A' and (resid 15 through 49 )
19X-RAY DIFFRACTION19chain 'A' and (resid 58 through 128 )
20X-RAY DIFFRACTION20chain 'A' and (resid 129 through 318 )
21X-RAY DIFFRACTION21chain 'A' and (resid 336 through 350 )
22X-RAY DIFFRACTION22chain 'B' and (resid 93 through 118 )
23X-RAY DIFFRACTION23chain 'B' and (resid 119 through 250 )
24X-RAY DIFFRACTION24chain 'B' and (resid 251 through 372)
25X-RAY DIFFRACTION25chain 'C' and (resid 15 through 49 )
26X-RAY DIFFRACTION26chain 'C' and (resid 58 through 128 )
27X-RAY DIFFRACTION27chain 'C' and (resid 129 through 318 )
28X-RAY DIFFRACTION28chain 'C' and (resid 336 through 350 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more