[English] 日本語
Yorodumi
- PDB-4ivw: Crystal Structure of the Estrogen Receptor alpha Ligand-binding D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ivw
TitleCrystal Structure of the Estrogen Receptor alpha Ligand-binding Domain in Complex with Constrained WAY-derivative, 6b
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Nuclear hormone receptor / Transcription factor / Ligand-binding / Nucleus
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / regulation of lipid metabolic process / androgen metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / 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 / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / stem cell differentiation / nuclear receptor binding / nuclear estrogen receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-1GJ / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Parent, A.A. / Cavett, V. / Nowak, J. / Hughes, T.S. / Kojetin, D.J. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Ligand binding dynamics rewire cellular signaling via Estrogen Receptor-alpha
Authors: Srinivasan, S. / Nwachukwu, J.C. / Parent, A.A. / Cavett, V. / Nowak, J. / Hughes, T.S. / Kojetin, D.J. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Estrogen receptor
C: Nuclear receptor coactivator 2
B: Estrogen receptor
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7006
Polymers58,9324
Non-polymers7692
Water2,486138
1
A: Estrogen receptor
C: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8503
Polymers29,4662
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area11950 Å2
MethodPISA
2
B: Estrogen receptor
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8503
Polymers29,4662
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-8 kcal/mol
Surface area11670 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-26 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.480, 81.400, 58.602
Angle α, β, γ (deg.)90.00, 109.82, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 28189.229 Da / Num. of mol.: 2 / Fragment: Ligand-binding Domain, UNP residues 303-549 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1276.530 Da / Num. of mol.: 2
Fragment: Receptor-interacting peptide, UNP residues 687-696
Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-1GJ / 4-[2-benzyl-7-(trifluoromethyl)-2H-indazol-3-yl]benzene-1,3-diol


Mass: 384.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H15F3N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 15% PEG 3350, 0.05M magnesium chloride, 0.067M sodium chloride, 0.1M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2012
RadiationMonochromator: Side scattering bent cube I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. all: 29295 / Num. obs: 29295 / % possible obs: 97.16 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 37.59 Å2 / Rsym value: 0.114 / Net I/σ(I): 15.19
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.36 / % possible all: 90.58

-
Processing

Software
NameVersionClassification
Blu-Iceicedata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→46.141 Å / SU ML: 0.46 / σ(F): 0 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 1906 6.81 %Random
Rwork0.1846 ---
all0.1876 27983 --
obs0.1876 27983 92.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.233 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2459 Å20 Å23.0084 Å2
2--3.6704 Å2-0 Å2
3----2.4245 Å2
Refinement stepCycle: LAST / Resolution: 2.06→46.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 56 138 4037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054025
X-RAY DIFFRACTIONf_angle_d0.7875467
X-RAY DIFFRACTIONf_dihedral_angle_d14.5051502
X-RAY DIFFRACTIONf_chiral_restr0.053643
X-RAY DIFFRACTIONf_plane_restr0.003679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.10420.36261090.25711528X-RAY DIFFRACTION76
2.1042-2.16110.26171270.21891698X-RAY DIFFRACTION86
2.1611-2.22470.25891280.20351720X-RAY DIFFRACTION86
2.2247-2.29650.23791290.19871843X-RAY DIFFRACTION93
2.2965-2.37860.25871340.20611885X-RAY DIFFRACTION93
2.3786-2.47380.24531420.20311875X-RAY DIFFRACTION94
2.4738-2.58640.28981480.20551902X-RAY DIFFRACTION96
2.5864-2.72270.26581400.21131919X-RAY DIFFRACTION95
2.7227-2.89330.24881350.2131879X-RAY DIFFRACTION94
2.8933-3.11660.23791450.19971964X-RAY DIFFRACTION98
3.1166-3.43020.27491420.1941972X-RAY DIFFRACTION98
3.4302-3.92630.21821430.16581943X-RAY DIFFRACTION97
3.9263-4.94580.17411360.14431941X-RAY DIFFRACTION95
4.9458-46.1410.20521480.18292008X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.56932.1902-0.69221.8982.01577.9034-0.9351-0.49760.04010.4177-0.055-0.3273-1.55340.87031.20970.74770.0546-0.09210.51220.04320.87673.619827.81480.6623
25.4838-4.5068-1.92454.05951.58681.07280.79051.11150.9883-0.9738-0.775-0.4071-0.286-0.3771-0.00120.42380.0474-0.03810.48880.0660.34133.90214.1829-6.564
38.2117-2.9181-1.76997.22821.25815.9789-0.0031.6733-0.6832-1.129-0.9514-0.29580.99510.78290.26610.81050.17570.16290.599-0.05260.340221.0551-4.1016-9.9843
49.1810.1995-0.21014.93963.49883.33372.13091.4537-0.1747-0.1920.8963-0.42470.3928-0.5894-2.46590.88410.14630.01630.63060.03520.980724.9606-15.1274-1.4967
59.542-6.67853.93766.7353-3.4146.0045-0.05790.137-0.2907-0.56440.21780.26490.01020.4628-0.21960.25580.0267-0.00240.38980.02210.35524.4474-2.3565-0.0613
64.7697-0.725-1.00187.04591.72493.96180.20470.78860.8826-0.8477-0.2028-0.3836-0.4573-0.00840.03660.3569-0.02390.01360.2950.07190.489615.376117.41540.1083
72.8472-0.3642-0.1934.11560.45022.3476-0.04630.1483-0.27530.112-0.01870.00640.3079-0.07180.07630.31090.0087-0.01550.30040.00590.273113.8516-1.54252.3633
82.4881-2.88771.47394.55140.03155.77040.00760.1363-1.01720.21680.07850.10120.86140.2692-0.0560.4730.01660.0230.20150.04480.381410.3494-9.20597.8516
95.1354-0.0801-0.44445.7591.40363.04610.16470.3645-0.18960.1695-0.01390.0623-0.0557-0.2841-0.1380.24220.0267-0.01520.32310.0260.25653.79717.21822.7206
105.41121.66084.54441.56840.13825.4109-0.686-1.62280.88240.51720.75271.7538-1.29620.3620.5510.71330.01860.25550.7435-0.03910.77237.58220.129813.0931
117.83741.67181.26155.6451.90133.60540.11720.18470.1051-0.1076-0.29550.62550.1319-0.27320.17870.29250.0876-0.04660.3569-0.04970.365-7.282511.71693.2697
126.0301-1.97412.69231.1126-0.56611.29960.02680.14520.2833-0.1027-0.1650.00420.2066-0.03920.11270.3558-0.00880.02490.3378-0.02430.32.73982.332611.1815
134.1260.7712-2.4123.4397-2.77125.80110.0219-1.8813-0.99870.735-0.2766-0.88140.39690.80250.17970.5717-0.0057-0.0620.58480.04790.407621.9123-1.130115.03
141.74320.4264-2.01935.76622.49223.91620.6829-0.0553-0.6119-0.6106-0.4195-0.34711.66042.4659-0.42750.8880.3419-0.20810.81520.04230.813131.7794-3.882711.7713
152.2908-1.8037-1.84478.61741.51546.8801-0.446-0.2721-0.2352-0.05230.4719-1.20070.7760.684-0.05710.30730.0125-0.02170.41810.02420.526727.98116.10428.7487
163.81045.72061.67149.47843.46922.56930.18890.5596-0.28710.82020.31081.01950.4143-0.0759-0.65160.7337-0.2852-0.02691.0358-0.04440.798-17.4785-5.741321.9476
178.0081-1.4845.66272.6519-1.13469.53840.2729-0.6126-0.38740.24790.47960.38280.4881-0.648-0.55410.3771-0.00510.03270.55740.05980.5784-13.62994.410629.4662
183.43574.28593.47266.84612.45176.21190.2958-1.5913-0.65830.0524-0.0436-1.0878-0.7050.12320.06980.59110.0502-0.04820.7981-0.07450.496110.245911.00646.8453
192.78171.2649-0.70696.56792.37058.17040.2249-1.24240.09920.75650.067-0.640.150.6549-0.23020.46330.0883-0.02620.5038-0.04810.414511.74843.952140.2537
202.2592-0.5834-0.12184.74951.57545.0585-0.0922-0.0845-0.41920.0222-0.13420.47650.4566-0.19330.22020.3679-0.02550.01160.35220.04030.3277-0.0085-1.763128.6712
214.04430.8874-2.77048.3079-1.24422.1352-0.1324-0.7450.61360.16140.36770.2641-0.78430.5052-0.35710.5145-0.0132-0.03710.6026-0.08480.38367.400916.685337.1277
223.7221-0.9622-3.23514.04671.20143.4806-0.1799-0.53190.76490.17740.5437-1.1657-1.04821.1264-0.39460.5729-0.19090.0020.4798-0.13810.521814.068315.295128.2592
232.63260.53361.2476.6449-0.98025.24940.1204-0.23290.3149-0.4254-0.0253-0.3667-0.2203-0.343-0.04740.279-0.0315-0.0060.3203-0.03240.2508-3.27938.129623.4783
240.8423-0.22070.04450.1411-0.51173.36060.41590.53140.8644-0.55850.34350.4459-0.5655-0.36240.9261.54530.33581.51941.24330.84180.79361.7771-11.574315.0104
258.71170.7439-4.85162.2409-0.45212.9156-0.93170.4203-1.2267-0.70970.38130.90181.9687-0.46070.40830.88-0.20840.12070.70270.02380.6978-6.96-9.557814.9627
263.52710.9859-0.60013.7212-0.85122.98520.00440.21350.09030.05230.04410.4026-0.2902-0.8730.04890.25010.0326-0.01080.4099-0.02920.2799-9.877111.730215.0431
278.1799-1.82370.45896.0364-0.88115.2047-0.4745-0.32880.0234-0.02540.1099-0.75670.06940.32190.1550.3368-0.02050.06840.3311-0.03270.383612.90734.453522.9729
281.27721.06781.60013.4179-0.59343.4533-0.3827-1.89820.6754-0.3762-0.01280.6421.15551.0916-0.52080.60360.3502-0.14851.5705-0.18791.071123.9219-2.116734.8594
295.69784.6317-5.23175.1201-3.9294.87540.8032-1.8846-0.79331.6173-0.3422-2.18891.07591.1803-0.62530.59060.099-0.17770.76180.05770.767114.5131-5.81537.4112
306.59434.98425.86993.80174.63156.5577-0.1730.9608-1.48380.7112-0.1824-0.01590.63571.720.06620.6190.07750.06880.55090.10420.851613.5208-7.20527.6634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 303:309)
2X-RAY DIFFRACTION2(chain A and resid 310:325)
3X-RAY DIFFRACTION3(chain A and resid 326:331)
4X-RAY DIFFRACTION4(chain A and resid 332:339)
5X-RAY DIFFRACTION5(chain A and resid 340:354)
6X-RAY DIFFRACTION6(chain A and resid 355:373)
7X-RAY DIFFRACTION7(chain A and resid 374:415)
8X-RAY DIFFRACTION8(chain A and resid 416:437)
9X-RAY DIFFRACTION9(chain A and resid 438:457)
10X-RAY DIFFRACTION10(chain A and resid 458:476)
11X-RAY DIFFRACTION11(chain A and resid 477:501)
12X-RAY DIFFRACTION12(chain A and resid 502:518)
13X-RAY DIFFRACTION13(chain A and resid 519:527)
14X-RAY DIFFRACTION14(chain A and resid 528:533)
15X-RAY DIFFRACTION15(chain A and resid 534:548)
16X-RAY DIFFRACTION16(chain B and resid 304:310)
17X-RAY DIFFRACTION17(chain B and resid 311:324)
18X-RAY DIFFRACTION18(chain B and resid 325:336)
19X-RAY DIFFRACTION19(chain B and resid 337:356)
20X-RAY DIFFRACTION20(chain B and resid 357:396)
21X-RAY DIFFRACTION21(chain B and resid 397:410)
22X-RAY DIFFRACTION22(chain B and resid 411:435)
23X-RAY DIFFRACTION23(chain B and resid 436:458)
24X-RAY DIFFRACTION24(chain B and resid 459:468)
25X-RAY DIFFRACTION25(chain B and resid 469:477)
26X-RAY DIFFRACTION26(chain B and resid 478:509)
27X-RAY DIFFRACTION27(chain B and resid 510:527)
28X-RAY DIFFRACTION28(chain B and resid 528:533)
29X-RAY DIFFRACTION29(chain B and resid 534:542)
30X-RAY DIFFRACTION30(chain B and resid 543:548)

+
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