[English] 日本語
Yorodumi
- PDB-3os9: Estrogen Receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3os9
TitleEstrogen Receptor
ComponentsEstrogen receptor
KeywordsSIGNALING PROTEIN / Estrogen receptor complex
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / Nuclear Receptor transcription pathway / beta-catenin binding / response to estrogen / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / ATPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KN1 / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsBruning, J. / Parent, A.A. / Gil, G. / Zhao, M. / Nowak, J. / Pace, M.C. / Smith, C.L. / Afonine, P.V. / Adams, P.D. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Coupling of receptor conformation and ligand orientation determine graded activity.
Authors: Bruning, J.B. / Parent, A.A. / Gil, G. / Zhao, M. / Nowak, J. / Pace, M.C. / Smith, C.L. / Afonine, P.V. / Adams, P.D. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionSep 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,53712
Polymers117,8624
Non-polymers2,6748
Water3,909217
1
A: Estrogen receptor
C: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2686
Polymers58,9312
Non-polymers1,3374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-33 kcal/mol
Surface area19040 Å2
MethodPISA
2
B: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2686
Polymers58,9312
Non-polymers1,3374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-33 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.904, 59.058, 93.761
Angle α, β, γ (deg.)86.64, 74.64, 63.43
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resid 306:329 or resid 332:415 or resid 420:461 or resid 465:526 or resid 533:546)
211chain B and (resid 306:329 or resid 332:415 or resid 420:461 or resid 465:526 or resid 533:546)
112chain C and (resid 306:329 or resid 332:415 or resid 420:461 or resid 471:526 or resid 533:546)
212chain D and (resid 306:329 or resid 332:415 or resid 420:461 or resid 471:526 or resid 533:546)

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29465.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Chemical
ChemComp-KN1 / 4-[1-allyl-7-(trifluoromethyl)-1H-indazol-3-yl]benzene-1,3-diol


Mass: 334.293 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H13F3N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: see publication, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9764 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.303→20 Å / Num. all: 39541 / Num. obs: 39541 / % possible obs: 91.42 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.303→20 Å / SU ML: 0.33 / σ(F): 1.96 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 1975 5.01 %
Rwork0.2048 --
obs0.207 39460 91.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.197 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.9713 Å2-2.9478 Å2-1.2047 Å2
2---15.025 Å24.1596 Å2
3---9.0536 Å2
Refinement stepCycle: LAST / Resolution: 2.303→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6961 0 192 217 7370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027411
X-RAY DIFFRACTIONf_angle_d0.6710079
X-RAY DIFFRACTIONf_dihedral_angle_d13.7042636
X-RAY DIFFRACTIONf_chiral_restr0.0431168
X-RAY DIFFRACTIONf_plane_restr0.0021226
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1747X-RAY DIFFRACTIONPOSITIONAL
12B1747X-RAY DIFFRACTIONPOSITIONAL0.019
21C1598X-RAY DIFFRACTIONPOSITIONAL
22D1598X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3026-2.36010.35171060.28891827X-RAY DIFFRACTION63
2.3601-2.42380.33851180.29542290X-RAY DIFFRACTION78
2.4238-2.4950.28821050.27452476X-RAY DIFFRACTION84
2.495-2.57540.30251650.25532601X-RAY DIFFRACTION89
2.5754-2.66720.28961410.23672665X-RAY DIFFRACTION92
2.6672-2.77370.2691500.24562742X-RAY DIFFRACTION94
2.7737-2.89960.27181470.22712792X-RAY DIFFRACTION95
2.8996-3.0520.28471300.22452851X-RAY DIFFRACTION97
3.052-3.24250.27361690.21512854X-RAY DIFFRACTION98
3.2425-3.49160.24971490.19842912X-RAY DIFFRACTION98
3.4916-3.84070.21611460.17442864X-RAY DIFFRACTION98
3.8407-4.39140.19481350.16532920X-RAY DIFFRACTION99
4.3914-5.51350.19961640.17152896X-RAY DIFFRACTION99
5.5135-20.03780.25741500.21122795X-RAY DIFFRACTION95
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)
11.80641.28671.03732.9678-1.97423.98770.04731.85920.2858-0.4787-0.265-1.1302-0.25350.00540.16280.27480.07390.10430.58060.11130.75069.774-20.0086-70.8569
21.9576-1.4195-1.49561.24660.56893.5281-0.7272-0.15590.1112-1.29650.1567-0.4041.10480.49230.4250.53230.0391-0.03030.25670.07880.5436-3.0137-35.9638-68.1811
33.6215-2.062-0.70942.8604-1.4242.56351.50851.0001-1.3328-0.8562-0.4624-1.56350.8292-0.9035-1.14031.5926-0.1896-0.05940.6574-0.15171.46-16.6547-48.7083-65.0602
40.7619-1.4662-0.38974.3831.21640.2822-0.44620.2073-1.0137-0.1895-0.02010.37761.3973-0.09930.29920.7475-0.16740.00320.5804-0.10820.5245-20.7083-40.5307-63.0851
50.9201-0.402-0.05721.2967-0.03610.3771-0.30490.26030.17820.4810.32890.0873-0.0633-0.03150.05990.28170.07670.03850.2776-0.03710.4331-3.1745-31.7553-59.9647
61.641.1639-0.27753.7796-1.21332.60450.3630.0201-0.2745-0.0586-0.1139-0.296-0.02360.0992-0.16380.31090.05260.00180.3534-0.01930.4163-4.8223-23.4896-61.5075
72.0235-0.76631.83368.5787-2.73532.3234-0.2201-0.38490.6364-1.85220.44220.64360.8615-0.39730.060.59690.0375-0.05970.3562-0.01430.6666-15.2215-36.1097-75.3926
86.6869-0.46020.27131.0231-0.37552.12310.07780.748-0.0114-1.16390.2487-0.34540.964-0.1502-0.19930.7342-0.1924-0.19310.5983-0.03230.5642-24.1682-35.5496-74.8603
94.34252.71312.28274.938-1.22774.1368-0.253-1.78570.30010.2974-0.7772-1.0693-0.353-2.35120.62521.0738-0.0056-0.19350.95-0.4031.3032-27.9702-34.697-67.3818
101.64440.97940.64633.4578-2.14912.2278-0.01290.23380.0696-0.69090.40550.6520.2836-0.5228-0.37790.3796-0.0087-0.12050.4139-0.0160.5994-19.2956-24.772-75.2023
115.97460.40251.52122.0887-0.79561.2512-0.82141.56520.0251-1.21540.39380.03260.96550.64680.2930.9632-0.06980.15270.3795-0.01890.4111-4.5733-22.5415-80.8757
120.88380.65320.00750.525-0.24120.8218-0.06610.3054-0.0343-0.0983-0.3859-0.4827-0.0894-0.08980.3370.32420.05130.01190.3938-0.05910.4329-3.7409-19.4019-67.6042
130.4104-0.76021.06831.533-1.94352.71831.8696-1.07881.35281.06440.04411.36550.6904-0.0618-1.28471.51150.24980.2531.42550.30590.7311-5.9656-10.1796-54.5091
141.9127-1.57992.10735.8252-4.89495.33530.20731.23850.9141.6393-1.0455-0.73650.56510.71221.01321.7087-0.07720.00420.7558-0.17760.77243.4081-7.5584-50.6241
159.74656.4953-6.20935.2531-3.94413.96260.8835-0.46272.9511-0.20640.62090.5895-2.4030.8199-0.31940.75830.0259-0.20140.678-0.14540.74422.9654-9.6181-59.6676
161.8993-0.5591-1.17454.4585-0.99231.69050.08270.23910.1616-0.7091-0.0332-0.47630.11470.1735-0.04840.42890.02270.08760.45380.00270.3237-1.275-12.2629-78.1915
174.19161.0124-3.30135.14793.55136.6004-0.69120.3825-0.33580.65390.11680.6890.8067-0.1380.17820.41270.0356-0.01390.33710.01940.5104-18.1202-19.1594-65.1471
183.95223.5769-3.1377.76950.38155.24610.66650.69870.61310.9771-0.5081-0.08720.8604-2.2111-0.09260.9679-0.19420.18970.61570.10371.1946-23.9478-26.5307-55.7327
193.6703-3.17522.37863.93210.15685.89112.4077-1.77251.4068-0.3413-0.7601-1.24811.6271-0.0904-1.24621.2607-0.3920.22580.56380.00360.6349-9.0312-27.1966-48.8534
207.6971-0.72890.89361.04960.66740.9079-0.341-1.68290.6748-1.98510.33160.550.226-0.1118-0.07141.0117-0.11690.00840.5808-0.00950.3952-0.4134-29.3495-50.1722
210.23620.2611-0.95563.0637-2.68864.5872-0.05380.31690.6657-0.1447-1.347-1.31250.36080.43160.99340.37860.04210.03390.69420.05440.686710.0022-22.4619-18.3449
221.50921.80390.24272.13440.86592.8505-0.1701-0.30430.43960.5886-0.1368-0.8334-0.8780.67090.22450.6124-0.104-0.05430.41430.04840.6293-2.9174-6.4077-20.57
234.04442.65311.2191.79180.7530.46250.8608-1.640.71190.9119-0.7466-0.3380.6265-0.12750.15011.381-0.4657-0.21652.28440.61561.2962-16.67635.9766-23.7001
242.52081.3559-0.79483.646-1.85030.9379-0.7021-1.29331.1674-0.71691.56430.15660.72460.6513-0.34591.06970.0130.02550.658-0.26330.9672-25.78060.6251-23.5449
258.12764.68040.56126.92890.69141.9695-0.3796-1.39881.1504-0.9035-0.281.36680.94480.38950.83640.58420.096-0.02340.7915-0.19510.6356-20.7845-3.4272-26.735
264.39961.7987-0.52491.81451.36362.93410.14990.7557-0.7593-0.45930.0382-0.2596-0.067-0.3994-0.22150.5693-0.0632-0.02310.3744-0.00710.4083-8.9546-6.377-28.9233
271.5027-0.44221.35432.4686-0.76271.3450.20420.02820.0507-0.0478-0.1422-0.0750.17470.0623-0.0530.311-0.00530.02380.3412-0.01190.3946-3.9326-18.1253-27.4439
281.5657-0.8632-1.43356.7215-2.77753.3472-0.05710.03530.29692.61650.3850.4098-1.6584-0.1879-0.13890.77060.01590.05390.3387-0.1010.5335-16.2472-5.9663-13.4449
292.4076-1.75131.34671.2175-0.88030.86611.20911.9612-1.3130.03180.11631.1148-0.1171-1.0951-0.91230.56220.14770.28010.83590.0061.4326-27.6126-8.5942-16.9629
302.0305-2.1063.4292.0362-7.9882.0061-1.3039-2.25252.7020.24742.02230.39921.5962-3.1932-0.71910.1557-0.16590.11070.72720.20151.0217-25.1014-14.8245-19.5376
313.1582-1.22791.6432.7254-1.30331.336-0.386-0.98620.41720.70820.35670.3122-1.2784-0.3792-0.07840.62570.0344-0.01160.4457-0.00760.4039-15.5068-19.3901-10.2844
323.4186-1.4829-2.57320.65960.94632.4376-0.93580.1096-0.57911.642-0.64360.38941.8093-0.50961.04420.8283-0.0882-0.02510.3825-0.10280.629-2.8602-19.1681-10.7047
331.8569-0.08060.49381.3852-2.29326.7666-0.4009-0.08030.3163-0.1611-0.61920.17081.0487-0.30340.74420.3694-0.05990.0370.3146-0.11230.521-4.1236-24.6514-24.0364
342.3145-2.027-0.94381.67550.54732.28230.41030.3188-2.3309-0.5966-0.75410.36492.03740.21520.00071.1803-0.1473-0.04690.72720.21111.0252-1.3821-32.9817-35.2855
357.804-7.59631.13139.901-3.60072.71990.9413-0.6082-2.1923-0.2609-0.0566-0.09242.17362.5356-0.45260.596-0.02750.05270.5818-0.09210.58663.3046-32.7891-28.8479
360.20930.7051.49532.20342.62645.60.2130.0001-0.140.6815-0.0172-0.57040.92331.4229-0.19650.4764-0.0668-0.04480.5533-0.02160.43593.7734-28.4485-12.8884
371.86130.62971.32090.45710.3921-0.0052-0.1446-0.3760.08230.42140.01630.10840.3314-0.15080.14060.49570.05240.03430.40590.02130.3406-8.547-29.5195-11.8275
385.9012-2.80974.6944.4195-1.1914.07330.0692-0.46360.012-2.7973-0.26882.2497-1.1648-2.27950.01720.446-0.0515-0.27790.38770.01141.0614-21.0201-20.8207-28.443
394.578-1.9773.79899.7285-0.40755.85650.492-1.3961-1.933-1.695-1.53720.3264-0.147-1.9840.67340.85030.1173-0.28380.4950.19711.3126-23.2915-15.2114-34.0104
404.2779-0.0321.12854.1418-2.81032.44151.27571.60070.6074-1.5496-0.19221.07250.685-0.2899-0.71390.89730.21490.010.38230.04630.3686-4.5518-14.0446-39.2186
413.21810.15931.77760.99020.49494.278-1.19091.08810.44670.27180.4591-0.0489-0.20231.64310.40831.0266-0.0267-0.04590.31380.05260.1074-15.88232.3603-88.018
421.4545-0.1914-0.46391.9060.38450.35440.4010.07360.374-2.2871-0.38390.08010.07520.3913-0.0421.0053-0.00930.07260.34030.02020.2496-15.00937.9793-79.8331
432.5489-0.2064-0.39193.22583.10143.22580.42940.29760.1346-0.8315-0.26020.3172-2.73120.2339-0.1070.61540.09350.04370.38450.06320.5686-24.469810.4521-65.4319
441.5343-0.475-0.55281.17120.18021.16671.38030.33250.2554-0.0634-0.75640.6260.80321.6385-0.35350.6419-0.1450.25680.73570.12650.7324-31.68024.4812-50.1211
450.3271-0.12940.58011.90371.14960.98620.0216-0.2801-0.8510.0258-0.35970.88780.1379-0.34610.18130.25150.07870.09860.3920.02490.6974-31.01873.2694-62.9238
467.69323.6847-1.41918.6858-1.10945.3948-1.00540.93681.5981-1.64641.40550.8131-3.9679-0.92890.24670.83060.1499-0.17090.4821-0.01730.316-26.83044.3255-75.8441
470.64090.5328-0.42350.8003-0.48870.635-0.1245-0.0797-0.419-0.53330.1687-0.07620.1843-0.313-0.03350.49290.0023-0.16790.4635-0.04420.5851-28.2149-5.5779-79.6534
483.0722-2.11-0.17572.868-0.0142.1506-0.1686-0.105-0.12690.41560.5208-0.2131-0.28580.2906-0.23780.35850.06420.0390.3430.01670.2794-19.66652.3001-58.755
494.02590.2195-1.93920.29480.24611.29320.7323-1.17150.5296-0.6065-0.69820.2888-2.2282-0.3521-0.13441.2830.0014-0.1620.75430.03710.3694-19.001-1.9843-45.4712
503.3042.8938-1.64984.033-1.75932.26030.3819-0.1621-0.66770.959-0.2675-0.53950.033-0.2787-0.17750.5122-0.0082-0.00380.39180.10650.4252-13.6379-4.4556-54.4386
515.3341-0.3216-2.78360.11450.07571.4663-0.1502-1.08530.4816-0.50990.40880.21160.36210.6945-0.00350.6734-0.092-0.030.55010.06410.3332-5.28782.0085-61.1194
522.34180.238-0.53041.33980.14350.38350.63370.3626-0.24110.4101-0.2599-0.035-0.3115-0.1634-0.23780.4976-0.0544-0.06630.2958-0.03710.2593-15.5602-1.2146-72.0767
534.2627-0.25173.33921.54860.53062.9421-1.39910.09220.20620.11830.1548-0.56131.4130.32370.7980.95130.02350.31960.84930.01091.2197-24.9631-17.3966-78.8578
540.74160.1221-0.64560.16810.20331.4217-0.7014-0.12920.3443-0.5540.7333-0.28481.22310.1448-0.00820.9518-0.134-0.23770.4906-0.07710.8909-26.4013-14.5079-87.3745
554.71620.8593-0.40527.1388-3.25664.9923-0.51260.6860.1569-2.50530.5963-0.16762.35621.2887-0.16820.7103-0.0142-0.07170.41460.02020.4072-17.2673-8.2492-83.9116
562.9719-2.97731.48043.8605-0.34523.3274-0.16790.240.5277-0.2347-0.01-0.6338-0.36050.54730.16140.3627-0.08760.06730.4091-0.00260.377-3.3847-1.5224-74.844
571.182-0.1895-0.70613.59841.40410.7833-0.03180.0419-0.4140.9175-0.0380.3949-0.10970.2346-0.04840.3540.04850.01830.33850.05030.3961-17.6203-11.2472-61.042
582.5976-1.0665-2.17312.52973.09124.1242-1.5488-0.9927-2.25510.6153-0.79430.69850.5432-0.30131.55671.6333-0.3047-0.1170.71180.35751.4971-28.3895-13.5553-56.4042
594.0063-1.75791.43837.8427-1.96211.04860.6514-0.29651.843-1.8488-0.30341.70621.23040.1363-0.31051.1647-0.18570.20051.0024-0.23421.8511-36.1982-8.9514-66.0729
600.4980.3534-0.24270.5767-0.98512.8710.1359-0.60640.9235-1.05931.06490.9944-0.1825-2.5705-0.92790.45030.0991-0.28170.9209-0.25351.4602-37.2135-1.8084-74.5776
612.39181.63970.36493.04820.64690.32590.3775-1.3520.22220.3594-0.9052-1.3454-0.12510.58210.49821.2945-0.13780.09990.58070.03880.2197-14.7255-46.0312-1.5862
620.9101-0.55680.79790.4722-0.53550.6830.10020.0458-0.8021-0.12470.29450.9874-0.2507-1.2523-0.47290.9168-0.07590.02160.36350.02810.2179-15.8675-50.0682-9.2687
632.57470.42760.19081.21040.38050.9795-0.4050.57320.48550.431-0.31541.0344-0.01480.54290.49950.4161-0.0735-0.08290.35010.08580.7777-25.0528-52.7348-24.0704
643.4222-1.493.77894.9322-0.27254.5597-0.3434-1.5752-0.1765-0.5780.72582.0668-0.8259-1.145-0.3720.4478-0.0372-0.22640.33470.13070.8796-31.4874-44.7075-34.8549
650.2818-0.0202-0.00280.20370.19321.881-0.68-0.07570.55960.0219-0.82890.94590.23280.2821.08760.3942-0.1472-0.04810.3939-0.01951.1637-30.8745-45.8632-22.6946
662.4308-1.2645-2.13911.13462.67178.0217-0.59750.0856-0.92371.5550.43960.45093.5853-0.07140.83010.6161-0.09930.29910.4258-0.0230.5439-26.8293-46.5821-12.8861
671.41021.1942-0.04072.2968-1.70141.23540.26470.07140.59320.1868-0.03740.82650.0109-0.1034-0.18640.2961-0.06430.10370.3638-0.06130.6171-24.6399-38.6759-17.4252
684.39753.62740.80667.4253.35962.08841.38581.2334-1.32240.22571.759-0.3425-0.880.096-1.54380.8099-0.04870.01940.7036-0.17240.673-11.6254-48.981-34.8263
692.1621-0.54321.85321.56611.55835.2066-0.35330.3382-1.4003-0.50270.64260.1357-0.954-0.3064-0.1270.5373-0.1249-0.07150.3830.02180.4547-21.6926-49.5369-36.0197
704.69543.33293.22643.00610.74656.4746-0.09551.0656-0.0482-0.91720.87250.32581.51441.8111-0.81671.361-0.1796-0.03920.81740.00690.5763-18.3401-40.834-43.7757
710.80950.9058-0.32731.7616-0.13020.5297-0.39881.105-0.325-0.64820.44620.3656-0.80690.097-0.07570.5999-0.0250.01390.45110.09810.2895-13.1177-38.3988-33.4822
722.8213.4068-1.94884.8458-0.06218.3492-1.03550.8092-1.6918-0.4296-0.0884-0.6965-0.9156-0.51710.88810.56160.0750.01940.50910.00960.477-5.1889-45.8031-25.9023
733.5518-2.0546-0.27365.86051.330.63310.3152-0.72940.30070.05240.1702-0.21140.2538-0.0331-0.37720.59250.00830.14460.3483-0.05850.3084-16.5697-40.1867-15.9926
742.891-2.505-0.57773.51461.75741.2415-1.38-0.5103-0.25911.25610.06911.54910.13040.7661.03291.0117-0.2748-0.01441.08750.09861.5228-23.664-27.6555-6.3257
750.5194-0.0625-0.75364.170.04071.9099-0.1827-1.7183-0.2579-0.1116-0.97531.16910.42450.35660.76010.920.10830.25580.3687-0.06520.7654-19.6075-31.9886-4.286
765.9963-3.5691-1.98896.35142.11750.88970.0748-0.82511.06210.91990.1693-0.80150.20960.3135-0.11420.48460.0214-0.01610.3180.00280.3027-6.145-42.3946-9.3242
770.1770.0799-0.03881.1887-0.33971.85750.22910.8424-0.5055-0.064-0.40090.25040.15070.74790.26710.27910.0205-0.05030.38250.01640.336-2.6921-37.3836-17.4875
783.50193.46161.62156.96761.46653.8807-0.0379-0.15751.2135-0.8462-0.34151.25140.27730.63950.35550.3825-0.0436-0.0190.3670.09320.4793-18.4262-31.003-27.7944
794.30662.20283.68516.06914.66148.3673-2.5319-1.321-0.3429-0.7477-1.37511.5648-1.3225-2.71552.11260.75950.2397-0.21360.83230.33981.4539-33.355-31.2083-25.2918
803.74480.1693-2.09212.0306-0.42471.2149-0.6427-0.31512.79071.529-0.04810.4280.6696-1.09170.40410.7617-0.14450.29940.8784-0.58051.7627-36.8254-39.0516-16.2001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 307:320
2X-RAY DIFFRACTION2chain A and resid 321:329
3X-RAY DIFFRACTION3chain A and resid 330:334
4X-RAY DIFFRACTION4chain A and resid 335:350
5X-RAY DIFFRACTION5chain A and resid 351:362
6X-RAY DIFFRACTION6chain A and resid 363:396
7X-RAY DIFFRACTION7chain A and resid 397:408
8X-RAY DIFFRACTION8chain A and resid 409:413
9X-RAY DIFFRACTION9chain A and resid 414:420
10X-RAY DIFFRACTION10chain A and resid 421:437
11X-RAY DIFFRACTION11chain A and resid 438:443
12X-RAY DIFFRACTION12chain A and resid 444:457
13X-RAY DIFFRACTION13chain A and resid 458:464
14X-RAY DIFFRACTION14chain A and resid 465:471
15X-RAY DIFFRACTION15chain A and resid 472:477
16X-RAY DIFFRACTION16chain A and resid 478:511
17X-RAY DIFFRACTION17chain A and resid 512:522
18X-RAY DIFFRACTION18chain A and resid 523:533
19X-RAY DIFFRACTION19chain A and resid 534:539
20X-RAY DIFFRACTION20chain A and resid 540:546
21X-RAY DIFFRACTION21chain B and resid 306:320
22X-RAY DIFFRACTION22chain B and resid 321:329
23X-RAY DIFFRACTION23chain B and resid 330:334
24X-RAY DIFFRACTION24chain B and resid 335:340
25X-RAY DIFFRACTION25chain B and resid 341:346
26X-RAY DIFFRACTION26chain B and resid 347:356
27X-RAY DIFFRACTION27chain B and resid 357:396
28X-RAY DIFFRACTION28chain B and resid 397:411
29X-RAY DIFFRACTION29chain B and resid 412:420
30X-RAY DIFFRACTION30chain B and resid 421:426
31X-RAY DIFFRACTION31chain B and resid 427:438
32X-RAY DIFFRACTION32chain B and resid 439:446
33X-RAY DIFFRACTION33chain B and resid 447:458
34X-RAY DIFFRACTION34chain B and resid 459:471
35X-RAY DIFFRACTION35chain B and resid 472:478
36X-RAY DIFFRACTION36chain B and resid 479:493
37X-RAY DIFFRACTION37chain B and resid 494:517
38X-RAY DIFFRACTION38chain B and resid 518:523
39X-RAY DIFFRACTION39chain B and resid 524:533
40X-RAY DIFFRACTION40chain B and resid 534:546
41X-RAY DIFFRACTION41chain C and resid 305:312
42X-RAY DIFFRACTION42chain C and resid 313:320
43X-RAY DIFFRACTION43chain C and resid 321:329
44X-RAY DIFFRACTION44chain C and resid 330:345
45X-RAY DIFFRACTION45chain C and resid 346:358
46X-RAY DIFFRACTION46chain C and resid 359:363
47X-RAY DIFFRACTION47chain C and resid 364:379
48X-RAY DIFFRACTION48chain C and resid 380:410
49X-RAY DIFFRACTION49chain C and resid 411:422
50X-RAY DIFFRACTION50chain C and resid 423:434
51X-RAY DIFFRACTION51chain C and resid 435:439
52X-RAY DIFFRACTION52chain C and resid 440:458
53X-RAY DIFFRACTION53chain C and resid 459:464
54X-RAY DIFFRACTION54chain C and resid 465:472
55X-RAY DIFFRACTION55chain C and resid 473:480
56X-RAY DIFFRACTION56chain C and resid 481:511
57X-RAY DIFFRACTION57chain C and resid 512:521
58X-RAY DIFFRACTION58chain C and resid 522:526
59X-RAY DIFFRACTION59chain C and resid 527:539
60X-RAY DIFFRACTION60chain C and resid 540:546
61X-RAY DIFFRACTION61chain D and resid 306:313
62X-RAY DIFFRACTION62chain D and resid 314:320
63X-RAY DIFFRACTION63chain D and resid 321:330
64X-RAY DIFFRACTION64chain D and resid 341:350
65X-RAY DIFFRACTION65chain D and resid 351:358
66X-RAY DIFFRACTION66chain D and resid 359:363
67X-RAY DIFFRACTION67chain D and resid 364:395
68X-RAY DIFFRACTION68chain D and resid 396:401
69X-RAY DIFFRACTION69chain D and resid 402:410
70X-RAY DIFFRACTION70chain D and resid 411:422
71X-RAY DIFFRACTION71chain D and resid 423:435
72X-RAY DIFFRACTION72chain D and resid 436:441
73X-RAY DIFFRACTION73chain D and resid 442:458
74X-RAY DIFFRACTION74chain D and resid 459:471
75X-RAY DIFFRACTION75chain D and resid 472:476
76X-RAY DIFFRACTION76chain D and resid 477:497
77X-RAY DIFFRACTION77chain D and resid 498:511
78X-RAY DIFFRACTION78chain D and resid 512:522
79X-RAY DIFFRACTION79chain D and resid 523:538
80X-RAY DIFFRACTION80chain D and resid 539:544

+
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