[English] 日本語
Yorodumi
- PDB-3sjq: Crystal structure of a small conductance potassium channel splice... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sjq
TitleCrystal structure of a small conductance potassium channel splice variant complexed with calcium-calmodulin
Components
  • Calmodulin
  • Small conductance calcium-activated potassium channel protein 2
KeywordsMETAL BINDING PROTEIN / protein-protein complex / EF hand / calmodulin / calcium binding
Function / homology
Function and homology information


Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / regulation of store-operated calcium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / : / regulation of high voltage-gated calcium channel activity / calcium-activated potassium channel activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex ...Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / regulation of store-operated calcium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / : / regulation of high voltage-gated calcium channel activity / calcium-activated potassium channel activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / positive regulation of potassium ion transport / inward rectifier potassium channel activity / establishment of protein localization to membrane / regulation of potassium ion transmembrane transport / negative regulation of high voltage-gated calcium channel activity / nitric-oxide synthase binding / positive regulation of DNA binding / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / alpha-actinin binding / regulation of synaptic vesicle endocytosis / regulation of neuronal synaptic plasticity / protein phosphatase activator activity / postsynaptic cytosol / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / regulation of cardiac muscle contraction / calcium channel regulator activity / detection of calcium ion / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / presynaptic cytosol / smooth endoplasmic reticulum / cellular response to interferon-beta / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / voltage-gated potassium channel complex / sperm midpiece / T-tubule / calcium channel complex / potassium ion transmembrane transport / calyx of Held / nitric-oxide synthase regulator activity / response to amphetamine / adenylate cyclase activator activity / regulation of heart rate / sarcomere / positive regulation of nitric-oxide synthase activity / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / calcium-mediated signaling / modulation of chemical synaptic transmission / potassium ion transport / sarcolemma / Schaffer collateral - CA1 synapse / cellular response to type II interferon / spindle pole / Z disc / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / disordered domain specific binding / myelin sheath / growth cone / protein autophosphorylation / vesicle / postsynaptic membrane / dendritic spine / transmembrane transporter binding / calmodulin binding / neuron projection / positive regulation of apoptotic process / protein domain specific binding / neuronal cell body / centrosome / calcium ion binding / protein kinase binding / glutamatergic synapse / cell surface / protein homodimerization activity / protein-containing complex
Similarity search - Function
Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / : ...Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-phenylurea / Calmodulin-1 / Calmodulin-1 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, M. / Pascal, J.M. / Zhang, J.-F.
CitationJournal: Structure / Year: 2012
Title: Structural basis for calmodulin as a dynamic calcium sensor.
Authors: Zhang, M. / Abrams, C. / Wang, L. / Gizzi, A. / He, L. / Lin, R. / Chen, Y. / Loll, P.J. / Pascal, J.M. / Zhang, J.F.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin
B: Calmodulin
C: Small conductance calcium-activated potassium channel protein 2
D: Small conductance calcium-activated potassium channel protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,77830
Polymers54,5924
Non-polymers2,18626
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-264 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.740, 65.630, 66.080
Angle α, β, γ (deg.)90.68, 110.45, 111.02
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc
Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / References: UniProt: P62161, UniProt: P0DP29*PLUS
#2: Protein Small conductance calcium-activated potassium channel protein 2 / SK2 / SKCa 2 / SKCa2 / KCa2.2


Mass: 10443.243 Da / Num. of mol.: 2 / Fragment: Calmodulin binding domain, UNP residues 412-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnn2 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / References: UniProt: P70604

-
Non-polymers , 5 types, 366 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-PHU / 1-phenylurea / Phenylurea


Mass: 136.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N2O
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.65
Details: 0.75 M Li2SO4, 0.5 M (NH4)2SO4, 0.1 M Sodium citrate pH 4.65 and Silver Bullets 22 reagent 70, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 53499 / Num. obs: 53499 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→2 Å / % possible all: 96.1

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G4Y

1g4y


Resolution: 1.9→19.994 Å / SU ML: 0.23 / σ(F): 2.04 / Phase error: 20.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 2675 5 %Random
Rwork0.1695 ---
obs0.1711 53459 97.96 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.671 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.497 Å2-0.1519 Å24.2567 Å2
2---2.5944 Å2-3.5547 Å2
3----0.9026 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 0 124 340 4083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143915
X-RAY DIFFRACTIONf_angle_d0.95177
X-RAY DIFFRACTIONf_dihedral_angle_d13.2661502
X-RAY DIFFRACTIONf_chiral_restr0.065563
X-RAY DIFFRACTIONf_plane_restr0.003679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.29292740.24354945X-RAY DIFFRACTION95
1.9679-2.04660.2382910.20035029X-RAY DIFFRACTION97
2.0466-2.13960.20662650.17475072X-RAY DIFFRACTION98
2.1396-2.25230.22042370.16245098X-RAY DIFFRACTION98
2.2523-2.39320.2022570.16625102X-RAY DIFFRACTION98
2.3932-2.57760.2312450.17765111X-RAY DIFFRACTION98
2.5776-2.83640.22312900.17855104X-RAY DIFFRACTION99
2.8364-3.24530.21982610.17095128X-RAY DIFFRACTION99
3.2453-4.0830.18312820.15535153X-RAY DIFFRACTION99
4.083-19.99460.17052730.16325042X-RAY DIFFRACTION98
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)
13.25231.67191.09875.88152.14821.45860.31291.3104-0.4957-1.1702-0.2143-0.2377-0.10180.026-0.13950.23940.0187-0.02370.43080.00540.2953.837553.5008-20.3789
22.61910.4241-0.54831.12790.83985.78460.0703-0.53720.55130.018-0.0369-0.0491-0.8038-0.0954-0.08350.05330.0185-0.0350.10020.00460.26371.976462.6074-5.9661
30.89490.7466-0.11540.82560.18920.43890.1286-0.73870.4170.2624-0.26570.39470.0461-0.58680.11180.1626-0.01590.02120.3464-0.06070.2865-6.237457.66231.9767
40.48391.09360.42494.7311.21424.7934-0.1575-0.6713-0.24130.2769-0.33110.38260.348-0.66870.26940.2524-0.0378-0.02210.33840.01760.2846-2.202149.90375.3027
51.41620.2207-0.72020.3117-0.19710.4157-0.0618-0.1555-0.15110.1726-0.0283-0.15490.4134-0.00430.11810.15240.0061-0.03550.2471-0.01460.28087.37152.3261-4.4922
60.6722-1.4424-1.98573.17313.85159.64730.05750.0172-1.0106-0.0806-0.59450.89630.8331-0.66290.00330.06550.03-0.06990.21720.00250.304-0.036345.5621-14.2115
71.17591.47710.52942.06990.2720.9658-0.40250.92380.6984-0.6990.1374-0.0398-0.39350.58040.18540.2413-0.0273-0.01480.407-0.02440.3675-8.00540.3604-19.5133
82.61090.79841.33151.83710.66430.8422-0.02030.5170.3769-0.221-0.12580.48830.2115-0.14970.14710.2782-0.0259-0.01810.2919-0.01740.2431-19.476434.6303-22.6995
92.0249-3.112-1.80136.03130.18670.69860.34211.8333-0.025-1.2401-0.74720.8575-0.0648-1.65060.2790.5605-0.0247-0.04440.5372-0.16910.2119-18.489125.6927-31.8173
104.95490.00021.07450.22910.91097.7808-0.04950.5586-1.28470.12260.1702-0.04972.62370.0817-0.10760.92960.0440.07750.1705-0.04150.4386-16.25617.4993-24.8128
111.49610.5040.363.95974.69555.61660.18250.2359-0.06241.72360.02690.02472.0301-0.2017-0.0210.8699-0.08130.02660.16810.03980.2626-19.458722.8142-14.7295
126.8104-5.0398-0.73817.41453.45162.8615-0.07480.158-0.15891.54510.5152-1.37181.28610.4954-0.51430.40390.1049-0.13040.2564-0.06930.3635-11.076129.6232-16.4131
133.1829-0.7255-0.90463.08191.660.97640.183-1.3340.88550.4192-0.0333-0.1672-0.31920.1639-0.18220.20080.0060.03380.4446-0.0330.28193.5378-11.25363.512
140.9179-0.9021-1.66562.29552.85644.5492-0.06020.5088-0.41920.2085-0.13980.15140.72-0.47990.10530.1532-0.00590.01170.2246-0.00890.28771.6042-19.9178-10.8312
150.19090.31230.12851.0065-0.03261.52270.02290.7287-0.309-0.1728-0.123-0.0239-0.1124-0.08170.11040.16620.0076-0.03160.327-0.03270.2476-6.3351-14.8697-18.8631
162.3644-0.71681.39340.7906-0.02831.08150.01140.88150.6571-0.3535-0.30290.0802-0.5994-0.13410.19160.26220.0588-0.02210.50640.0480.3288-2.4682-7.1709-22.1076
170.96050.0840.81790.08260.08120.67960.05850.1360.3511-0.1977-0.0153-0.0409-0.29420.14180.01680.15580.0060.02880.24820.02390.28266.4985-9.3308-11.4932
182.7493-1.2353-2.54021.86441.65792.62760.17970.04280.55130.3115-0.25450.7485-0.7918-0.4360.24180.2015-0.0280.04230.3447-0.07030.4454-1.3921-1.4954-1.4624
197.7311-5.45596.9849.6354-1.85327.95320.0251-0.4814-1.240.661-0.06740.89420.1626-0.98460.4623-0.0096-0.0205-0.00630.0865-0.07810.1793-9.52812.91483.5478
204.1256-3.2615-2.83924.67760.38974.69050.1671-0.0166-0.74980.3558-0.27291.3071-0.2423-0.42940.11780.2297-0.00420.08610.17930.01010.2935-20.68048.4886.208
213.3381-2.00620.8463.4529-0.47510.2449-0.2429-0.9999-0.01980.89550.01510.4211-0.3594-0.58370.08970.50760.01410.1340.2271-0.00760.2517-19.612817.180213.4456
220.83731.16670.69012.66483.56399.4917-0.2878-0.46890.235-0.0587-0.22310.6915-1.90380.39330.25620.7935-0.02240.2140.21270.01330.4143-16.861925.38388.17
231.66391.77050.12442.80921.58012.36730.2182-0.07780.4442-1.35560.14220.1289-1.35820.0324-0.32420.68140.04250.06870.21530.03070.3428-19.012717.519-2.21
248.4232-3.6321-5.70168.05754.52258.58-0.2203-0.42230.8816-1.78970.3698-2.6385-0.60540.8538-0.30820.3565-0.10230.20850.2704-0.090.5471-10.76913.715-0.4791
252.2995-0.6936-0.08563.2863-3.81035.2017-0.71670.42760.619-1.40250.8529-0.490.3741-0.35270.05920.6179-0.15480.09450.25720.01920.4037-4.941324.3513.1532
262.0801-0.45750.7852.4245-0.32840.44870.009-0.4526-0.34561.54930.0612-0.47420.27690.1029-0.1570.80040.0281-0.05420.30850.03270.2209-7.00968.485518.8064
271.96090.574-1.27550.2468-0.38591.7507-0.136-0.26140.82191.45630.2994-0.2752-0.04890.2738-0.1360.6905-0.0091-0.00250.20720.05760.4624-5.49526.945112.4689
283.9691-1.90941.41244.0481-1.51783.4180.7292-0.5984-0.42020.4505-0.00721.3986-0.0158-0.2153-0.66770.3308-0.0709-0.07590.39010.11690.6267-9.126438.89872.5059
290.8105-0.41650.4820.66690.19610.7837-0.03840.18-0.19520.13590.00880.30560.2207-0.0510.19020.1150.0051-0.01450.3092-0.01970.3072-6.825752.0019-10.4427
302.2059-0.6872-1.93850.65752.11337.93660.3138-0.3815-1.82531.79670.0289-0.3644-1.99220.4731-0.36381.05260.0949-0.25340.38270.28791.359-1.868214.3733-16.9918
312.3640.9827-3.53991.97210.36048.1678-0.640.0484-0.571-0.04380.4714-0.59040.3465-0.49330.18880.52830.09770.09820.29010.00470.3122-7.450127.0976-26.6952
321.39830.0302-0.170.9654-0.33180.7745-0.10170.47960.0885-0.17890.2303-0.6363-0.91280.1174-0.10410.94760.09160.24270.30370.06520.2709-5.776636.0746-38.0761
33-0.06740.6508-0.30826.5942-3.35581.63630.2179-0.02550.017-0.9754-0.11690.20380.06020.1605-0.08850.49650.02290.09050.23670.02010.4124-6.86339.2139-24.0579
340.38260.35030.03021.55960.50311.5969-0.1878-0.3156-0.06510.5705-0.2350.2086-0.2407-0.01670.31220.1757-0.0008-0.0110.33670.01720.3003-6.5261-12.607-3.7079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:12)
2X-RAY DIFFRACTION2(chain A and resid 13:26)
3X-RAY DIFFRACTION3(chain A and resid 27:42)
4X-RAY DIFFRACTION4(chain A and resid 43:53)
5X-RAY DIFFRACTION5(chain A and resid 54:71)
6X-RAY DIFFRACTION6(chain A and resid 72:79)
7X-RAY DIFFRACTION7(chain A and resid 80:86)
8X-RAY DIFFRACTION8(chain A and resid 87:99)
9X-RAY DIFFRACTION9(chain A and resid 100:116)
10X-RAY DIFFRACTION10(chain A and resid 117:128)
11X-RAY DIFFRACTION11(chain A and resid 129:136)
12X-RAY DIFFRACTION12(chain A and resid 137:147)
13X-RAY DIFFRACTION13(chain B and resid 2:12)
14X-RAY DIFFRACTION14(chain B and resid 13:26)
15X-RAY DIFFRACTION15(chain B and resid 27:42)
16X-RAY DIFFRACTION16(chain B and resid 43:53)
17X-RAY DIFFRACTION17(chain B and resid 54:73)
18X-RAY DIFFRACTION18(chain B and resid 74:80)
19X-RAY DIFFRACTION19(chain B and resid 81:87)
20X-RAY DIFFRACTION20(chain B and resid 88:98)
21X-RAY DIFFRACTION21(chain B and resid 99:116)
22X-RAY DIFFRACTION22(chain B and resid 117:128)
23X-RAY DIFFRACTION23(chain B and resid 129:138)
24X-RAY DIFFRACTION24(chain B and resid 139:146)
25X-RAY DIFFRACTION25(chain C and resid 414:428)
26X-RAY DIFFRACTION26(chain C and resid 429:454)
27X-RAY DIFFRACTION27(chain C and resid 455:469)
28X-RAY DIFFRACTION28(chain C and resid 470:475)
29X-RAY DIFFRACTION29(chain C and resid 476:493)
30X-RAY DIFFRACTION30(chain D and resid 415:419)
31X-RAY DIFFRACTION31(chain D and resid 420:435)
32X-RAY DIFFRACTION32(chain D and resid 436:453)
33X-RAY DIFFRACTION33(chain D and resid 454:481)
34X-RAY DIFFRACTION34(chain D and resid 482:492)

+
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