[English] 日本語
Yorodumi
- PDB-6lc1: Structural basis of NR4A1 bound to the human pituitary proopiomel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lc1
TitleStructural basis of NR4A1 bound to the human pituitary proopiomelanocortin gene promoter
Components
  • DNA
  • DNA (25-MER)
  • Nuclear receptor subfamily 4 group A member 1
KeywordsDNA BINDING PROTEIN/DNA / nuclear receptor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis ...neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / fat cell differentiation / skeletal muscle cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of cell cycle / cellular response to vascular endothelial growth factor stimulus / response to electrical stimulus / positive regulation of endothelial cell proliferation / response to amphetamine / lipopolysaccharide binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / presynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Orphan nuclear receptor, HMR type / Orphan nuclear receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Orphan nuclear receptor, HMR type / Orphan nuclear receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsJiang, L. / Chen, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81372904 and 81570537 China
National Natural Science Foundation of China81272971 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural basis of NR4A1 bound to the human pituitary proopiomelanocortin gene promoter.
Authors: Jiang, L. / Wei, H. / Yan, N. / Dai, S. / Li, J. / Qu, L. / Chen, X. / Guo, M. / Chen, Z. / Chen, Y.
History
DepositionNov 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation.pdbx_database_id_PubMed / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.2Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: DNA
J: Nuclear receptor subfamily 4 group A member 1
L: DNA (25-MER)
A: Nuclear receptor subfamily 4 group A member 1
C: DNA (25-MER)
D: Nuclear receptor subfamily 4 group A member 1
F: DNA
G: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,06916
Polymers71,5458
Non-polymers5238
Water00
1
I: DNA
J: Nuclear receptor subfamily 4 group A member 1
L: DNA (25-MER)
G: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0348
Polymers35,7734
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-36 kcal/mol
Surface area16840 Å2
MethodPISA
2
A: Nuclear receptor subfamily 4 group A member 1
C: DNA (25-MER)
D: Nuclear receptor subfamily 4 group A member 1
F: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0348
Polymers35,7734
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-110 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.822, 63.210, 91.762
Angle α, β, γ (deg.)109.980, 90.210, 89.540
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain F and (resid 2 through 11 or resid 13 through 26))
21(chain I and (resid 2 through 11 or resid 13 through 26))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11DGDGDADA(chain F and (resid 2 through 11 or resid 13 through 26))FG2 - 112 - 11
12DCDCDGDG(chain F and (resid 2 through 11 or resid 13 through 26))FG13 - 2613 - 26
21DGDGDADA(chain I and (resid 2 through 11 or resid 13 through 26))IA2 - 112 - 11
22DCDCDGDG(chain I and (resid 2 through 11 or resid 13 through 26))IA13 - 2613 - 26

-
Components

#1: DNA chain DNA


Mass: 7971.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein
Nuclear receptor subfamily 4 group A member 1 / Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR ...Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR / Orphan nuclear receptor TR3 / ST-59 / Testicular receptor 3


Mass: 9899.692 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A1, GFRP1, HMR, NAK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22736
#3: DNA chain DNA (25-MER)


Mass: 8002.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Ammonium sulfate, 10mM magnesium chloride, 50mM MES monohydrate pH 5.6, 20% w/v Polyethylene glycol 8K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.12→29.646 Å / Num. obs: 12751 / % possible obs: 92.1 % / Redundancy: 3.8 % / Rpim(I) all: 0.071 / Rrim(I) all: 0.136 / Net I/σ(I): 7
Reflection shellResolution: 3.12→3.232 Å / Mean I/σ(I) obs: 2.54 / Num. unique obs: 984 / Rpim(I) all: 0.181 / Rrim(I) all: 0.357

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cit

1cit


Resolution: 3.12→29.646 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 30.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 677 5.31 %
Rwork0.2093 12072 -
obs0.2125 12749 92.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.76 Å2 / Biso mean: 93.8968 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.12→29.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 2090 8 0 4779
Biso mean--92.65 --
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035065
X-RAY DIFFRACTIONf_angle_d0.737224
X-RAY DIFFRACTIONf_chiral_restr0.047786
X-RAY DIFFRACTIONf_plane_restr0.002578
X-RAY DIFFRACTIONf_dihedral_angle_d19.6912710
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11F468X-RAY DIFFRACTION17.4TORSIONAL
12I468X-RAY DIFFRACTION17.4TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1202-3.36080.38261140.3047213381
3.3608-3.69850.31861420.2843235190
3.6985-4.23230.33921270.2462251697
4.2323-5.32720.24781550.1953257999
5.3272-29.6460.2081390.1582249396
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)
19.0712-0.5854-2.0558.5682-4.78676.37361.3921-1.49371.86460.1353-2.3769-0.40740.533.0088-0.64291.0206-0.22750.18511.2899-0.12960.6823-38.856142.075941.2674
20.6558-0.85260.19661.8876-2.20144.02480.50270.56020.2545-0.65590.4617-0.1584-0.10370.5305-0.33131.3099-0.14440.29860.9314-0.04581.0701-32.794841.63416.4195
32.3919-0.8619-0.75825.0186-0.78755.5293-0.03540.4765-0.12290.3365-0.0790.81921.0156-0.7064-0.23750.9168-0.14270.24270.92580.0280.828-30.841542.2831-17.9641
44.345-0.1718-1.17481.1613-1.20523.6388-0.4073-0.6101-0.68781.07040.31890.8949-1.73140.4214-0.35351.245-0.11130.11640.78250.09930.8297-24.68157.9266-17.6609
53.64672.02020.80483.3839-0.39314.7863-0.0949-1.82690.54250.285-0.36941.2996-1.26410.6347-0.29751.0496-0.1730.16270.90420.08170.8694-21.355751.2314-13.1968
66.44640.0046-0.1316.3812-0.83216.5849-0.6914-0.1055-0.5590.88940.09150.52230.6710.9758-0.30670.5843-0.02310.01050.82410.03690.7701-20.992143.6971-22.0199
72.1121.8614-1.08451.6347-1.04914.3614-0.06911.30610.9580.5115-0.4343-0.1945-1.07660.4043-0.32850.8116-0.20060.05411.01030.07810.8964-17.419553.6514-31.9958
83.7966-0.481-0.11082.31410.30151.27170.04430.77770.2563-0.24230.62280.1708-0.28711.9033-0.35880.5351-0.14120.0241.2687-0.11230.5873-14.034551.456-25.3721
97.97873.39370.15712.8112.22423.406-0.0734-0.4192-0.164-0.43360.2741-0.76230.33441.9794-0.79260.6542-0.0245-0.3441.7096-0.57330.9069-12.372245.4556-15.6054
100.13990.4354-0.23451.4059-0.07733.4432-0.51870.1879-1.98511.0936-0.3091-2.42311.80581.5617-0.21381.06160.1730.19571.12990.17161.1759-18.077833.8387-12.8499
119.475.94747.79133.73694.88196.3536-2.3943-1.41081.50380.1209-0.73230.6929-0.0658-0.0957-1.48931.18710.34970.45011.14280.211.3466-23.109638.0537-5.1037
126.93351.64480.99165.5541-1.22093.9819-0.1859-0.5159-0.65490.019-0.17480.52381.5548-0.035-0.24730.9007-0.09140.21260.7539-0.05430.7352-28.825343.8318-27.7851
131.65010.0028-1.52780.8691.0315.76470.2384-0.70810.17251.0733-0.00120.3515-0.22310.3039-0.30471.348-0.19640.24430.93820.07720.8829-30.592542.2356-1.8768
143.3374-0.1258-2.05852.71493.15484.53140.4598-0.19830.6985-0.2470.5269-0.1844-0.84740.9322-0.28310.9185-0.16670.10080.7899-0.12560.8214-34.256141.611629.4704
151.92781.25070.0931.48390.83050.76-0.0162-0.65850.09660.8930.19510.9917-0.39820.0976-0.39010.95960.0752-0.10820.71020.1280.8734-48.5139.6995-14.0017
163.9646-1.35230.08362.153-0.86262.56050.73560.5644-0.94930.1046-0.2979-0.87910.3162-0.4572-0.34380.57380.108-0.08230.63480.00930.8003-43.780415.7228-18.9297
171.72220.96160.59011.34170.51610.42351.69530.6599-0.3994-0.3768-0.72810.5640.7156-0.9159-0.32570.71710.1658-0.05141.31610.09740.8853-46.43523.916-29.638
182.7148-1.2242-1.64820.57260.76041.01161.50681.6063-1.3269-0.426-0.2338-0.54281.2867-0.0495-0.13750.77370.034-0.42151.1922-0.23820.9191-54.1912.748-29.725
192.58660.39651.73774.23140.55381.24880.5684-0.1532-0.13010.0320.50320.8990.1066-0.5715-0.3540.60090.2238-0.02780.92730.06540.8556-53.02918.834-21.376
204.85454.43-3.1047.7466-4.80963.44490.92870.71541.44161.24120.92131.2821-1.1923-0.62671.37330.97050.15970.14230.04-0.4190.6918-42.122125.1452-13.6056
214.1038-0.6651-3.02131.8948-0.93767.82860.5764-1.3391-0.33671.7216-0.4794-0.3877-0.34991.7222-0.44260.84240.0185-0.15751.091-0.18531.0738-33.441522.2036-7.3647
223.4348-0.49690.47945.42372.51524.50230.4536-0.1935-0.4680.69830.4504-0.4512-0.1050.2385-0.30560.73950.1781-0.13990.7714-0.07260.8015-34.376811.9635-13.9434
233.59350.12281.79972.9098-1.16885.30530.13910.6677-0.0011-0.93730.0380.9585-0.6822-0.5512-0.1941.06070.0165-0.16420.7577-0.0110.8837-30.482410.720526.2558
241.6684-0.32111.31690.0421-0.17931.0546-1.2475-0.45240.5083-0.09050.79910.33221.6516-0.3632-0.37010.96530.1023-0.051.01280.08951.0234-24.3132-4.872730.9182
254.7476-0.8955-1.17622.9306-0.18453.9058-0.2013-0.3689-0.5247-0.4706-0.1235-0.07830.62731.324-0.35730.5530.0894-0.1170.77020.15880.7724-18.34454.42837.3045
263.6742.544-1.2615.94310.77041.0972-0.0079-1.2867-1.93320.01330.5923-0.08471.3678-1.9806-0.36861.05150.075-0.06710.93770.11221.1066-23.568-3.266244.3878
273.14440.75410.64990.8035-0.10751.3162-0.53460.22671.0428-0.28930.86030.33371.06941.8101-0.28740.53140.0227-0.0590.93750.08890.7522-14.06121.766738.8415
284.6241-2.45311.94711.4235-0.8063.94870.29020.8181.2647-0.10870.3022-1.16980.08941.9683-0.17660.7018-0.1941-0.03331.4094-0.02640.8852-13.09078.695728.8528
293.573-1.6321-1.03881.9689-0.94443.5784-0.3529-0.06580.8479-1.5054-0.3091-0.1975-2.06160.7304-0.28661.19-0.0708-0.16980.86040.16231.0566-20.635218.424623.7689
304.1006-0.51541.58113.379-2.75584.6950.2219-0.13090.189-0.4865-0.08070.2451-0.43660.0028-0.32190.9170.0511-0.19070.6912-0.05680.9226-30.27610.242924.8745
313.3740.43761.28532.47121.40863.78970.66430.5104-0.45180.1960.4286-0.42571.27860.5861-0.2770.9450.1331-0.19470.8548-0.16470.7981-34.389410.857-17.8825
322.77831.0540.27953.72030.62570.09160.665-0.52171.7076-0.3953-0.71411.247-0.06370.4352-0.42440.9839-0.11750.14850.80360.1281.2427-50.697146.251929.1692
334.01161.11530.73332.18050.56523.83630.548-0.07850.4056-0.3732-0.3407-0.5015-0.59211.2857-0.33430.75360.00170.17310.5891-0.03440.7636-44.377837.40330.3993
340.82360.24950.63821.0578-0.15822.19460.5971-0.72710.2801-0.0648-0.5921.5108-0.0017-0.3504-0.37511.171-0.105-0.01071.02590.11791.2688-53.832932.855843.8873
352.77630.10770.19751.6290.7470.4880.4642-1.03041.03660.4267-0.5487-0.012-0.8332-1.2201-0.41081.472-0.09170.23851.3104-0.45411.2354-52.589644.960241.5542
363.0029-0.97380.36873.2076-0.08282.83620.42450.73230.61550.2550.77390.85090.78620.4849-0.36460.8308-0.15530.07710.8330.0620.9695-52.978334.100637.3328
374.1942-0.6483-0.61770.4057-0.64481.40830.09442.0731-2.1667-0.4422-0.42870.35990.7752-0.2138-0.31980.7232-0.0121-0.1410.5529-0.14020.8281-42.222228.006427.0593
382.1666-1.09610.47961.9828-2.28154.261.42281.654-0.4689-1.1893-0.51980.20911.26091.4565-0.3441.1938-0.01810.10831.00360.12040.919-33.355231.233420.6478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'I' and (resid 1 through 5 )I1 - 5
2X-RAY DIFFRACTION2chain 'I' and (resid 6 through 15 )I6 - 15
3X-RAY DIFFRACTION3chain 'I' and (resid 16 through 26 )I16 - 26
4X-RAY DIFFRACTION4chain 'J' and (resid 265 through 275 )J265 - 275
5X-RAY DIFFRACTION5chain 'J' and (resid 276 through 284 )J276 - 284
6X-RAY DIFFRACTION6chain 'J' and (resid 285 through 297 )J285 - 297
7X-RAY DIFFRACTION7chain 'J' and (resid 298 through 319 )J298 - 319
8X-RAY DIFFRACTION8chain 'J' and (resid 320 through 330 )J320 - 330
9X-RAY DIFFRACTION9chain 'J' and (resid 331 through 335 )J331 - 335
10X-RAY DIFFRACTION10chain 'J' and (resid 336 through 345 )J336 - 345
11X-RAY DIFFRACTION11chain 'J' and (resid 346 through 350 )J346 - 350
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 5 )L1 - 5
13X-RAY DIFFRACTION13chain 'L' and (resid 6 through 15 )L6 - 15
14X-RAY DIFFRACTION14chain 'L' and (resid 16 through 25 )L16 - 25
15X-RAY DIFFRACTION15chain 'A' and (resid 266 through 280 )A266 - 280
16X-RAY DIFFRACTION16chain 'A' and (resid 281 through 296 )A281 - 296
17X-RAY DIFFRACTION17chain 'A' and (resid 297 through 303 )A297 - 303
18X-RAY DIFFRACTION18chain 'A' and (resid 304 through 321 )A304 - 321
19X-RAY DIFFRACTION19chain 'A' and (resid 322 through 331 )A322 - 331
20X-RAY DIFFRACTION20chain 'A' and (resid 332 through 342 )A332 - 342
21X-RAY DIFFRACTION21chain 'A' and (resid 343 through 351 )A343 - 351
22X-RAY DIFFRACTION22chain 'C' and (resid 1 through 15 )C1 - 15
23X-RAY DIFFRACTION23chain 'C' and (resid 16 through 25 )C16 - 25
24X-RAY DIFFRACTION24chain 'D' and (resid 265 through 275 )D265 - 275
25X-RAY DIFFRACTION25chain 'D' and (resid 276 through 312 )D276 - 312
26X-RAY DIFFRACTION26chain 'D' and (resid 313 through 319 )D313 - 319
27X-RAY DIFFRACTION27chain 'D' and (resid 320 through 330 )D320 - 330
28X-RAY DIFFRACTION28chain 'D' and (resid 331 through 336 )D331 - 336
29X-RAY DIFFRACTION29chain 'D' and (resid 337 through 350 )D337 - 350
30X-RAY DIFFRACTION30chain 'F' and (resid 1 through 15 )F1 - 15
31X-RAY DIFFRACTION31chain 'F' and (resid 16 through 26 )F16 - 26
32X-RAY DIFFRACTION32chain 'G' and (resid 266 through 275 )G266 - 275
33X-RAY DIFFRACTION33chain 'G' and (resid 276 through 296 )G276 - 296
34X-RAY DIFFRACTION34chain 'G' and (resid 297 through 311 )G297 - 311
35X-RAY DIFFRACTION35chain 'G' and (resid 312 through 319 )G312 - 319
36X-RAY DIFFRACTION36chain 'G' and (resid 320 through 329 )G320 - 329
37X-RAY DIFFRACTION37chain 'G' and (resid 330 through 342 )G330 - 342
38X-RAY DIFFRACTION38chain 'G' and (resid 343 through 351 )G343 - 351

+
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://pdbjlvh1.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