[English] 日本語
Yorodumi
- PDB-5dug: Crystal Structure of the ER-alpha Ligand-binding Domain in Comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dug
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with a Sulfoxide-bridged Oxabicyclic Heptene Sulfonate (SOBHS)-2 analog phenyl (1S,2S,4S,7S)-5,6-bis(4-hydroxy-2-methylphenyl)-7-thiabicyclo[2.2.1]hept-5-ene-2-sulfonate 7-oxide
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
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 / steroid binding / Regulation of lipid metabolism by PPARalpha / 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 estrogen receptor binding / nuclear 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 / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / 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-5FV / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.252 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. / Houtman, R. ...Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / Katzenellenbogen, J.A. / Zhou, H.B. / Nettles, K.W.
CitationJournal: Mol.Syst.Biol. / Year: 2016
Title: Predictive features of ligand-specific signaling through the estrogen receptor.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Nowak, J. / Wright, N.J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Nowak, J. / Wright, N.J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / Katzenellenbogen, J.A. / Zhou, H.B. / Nettles, K.W.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
A: Estrogen receptor
B: Estrogen receptor
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9266
Polymers61,9334
Non-polymers9932
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-30 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.140, 82.146, 58.354
Angle α, β, γ (deg.)90.000, 110.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 306:330 or resseq 336:458 or resseq 471:548 )
21chain B and (resseq 306:330 or resseq 336:458 or resseq 471:548 )

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
11LEULEUGLUGLUchain A and (resseq 306:330 or resseq 336:458 or resseq 471:548 )AA306 - 3309 - 33
12PROPROVALVALchain A and (resseq 306:330 or resseq 336:458 or resseq 471:548 )AA336 - 45839 - 161
13GLUGLUARGARGchain A and (resseq 306:330 or resseq 336:458 or resseq 471:548 )AA471 - 548174 - 251
21LEULEUGLUGLUchain B and (resseq 306:330 or resseq 336:458 or resseq 471:548 )BB306 - 3309 - 33
22PROPROVALVALchain B and (resseq 306:330 or resseq 336:458 or resseq 471:548 )BB336 - 45839 - 161
23GLUGLUARGARGchain B and (resseq 306:330 or resseq 336:458 or resseq 471:548 )BB471 - 548174 - 251

-
Components

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


Mass: 29299.535 Da / Num. of mol.: 2 / Fragment: ligand-binding domain / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 1666.943 Da / Num. of mol.: 2 / Fragment: Nuclear receptor-interacting peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-5FV / phenyl (1S,2S,4S,7S)-5,6-bis(4-hydroxy-2-methylphenyl)-7-thiabicyclo[2.2.1]hept-5-ene-2-sulfonate 7-oxide


Mass: 496.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24O6S2
#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: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

-
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 8, 2011
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: 2.252→50 Å / Num. obs: 22491 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.072 / Χ2: 1.804 / Net I/av σ(I): 27.175 / Net I/σ(I): 10.7 / Num. measured all: 85500
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.27-2.313.80.32711111.25999.8
2.31-2.353.80.24211451.231100
2.35-2.43.80.22810991.33899.9
2.4-2.453.80.19811071.30499.9
2.45-2.53.80.17111091.35100
2.5-2.563.80.17611501.34100
2.56-2.623.80.14610931.374100
2.62-2.693.80.13511231.582100
2.69-2.773.80.1211131.44799.9
2.77-2.863.80.11111191.442100
2.86-2.963.80.09711281.65599.9
2.96-3.083.80.0911231.786100
3.08-3.223.80.08511411.949100
3.22-3.393.80.07411142.0699.9
3.39-3.63.80.07111272.4299.9
3.6-3.883.70.06311362.59399.9
3.88-4.273.80.05711122.62399.9
4.27-4.893.80.05711362.64399.9
4.89-6.163.70.05511422.268100
6.16-503.60.04611632.48699.7

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QA8
Resolution: 2.252→46.185 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 1937 8.91 %
Rwork0.189 19804 -
obs0.1929 21741 95.89 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.61 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 159.39 Å2 / Biso mean: 44.7113 Å2 / Biso min: 7.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.1869 Å20 Å22.2935 Å2
2--1.3436 Å20 Å2
3----0.1567 Å2
Refinement stepCycle: final / Resolution: 2.252→46.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 68 138 4010
Biso mean--46.14 37.64 -
Num. residues----487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043991
X-RAY DIFFRACTIONf_angle_d1.2825424
X-RAY DIFFRACTIONf_chiral_restr0.089645
X-RAY DIFFRACTIONf_plane_restr0.007671
X-RAY DIFFRACTIONf_dihedral_angle_d14.8151473
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1707X-RAY DIFFRACTIONPOSITIONAL0.041
12B1707X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2523-2.30870.32481160.2341051116773
2.3087-2.37110.26461370.21691388152595
2.3711-2.44090.26161270.20791407153495
2.4409-2.51960.23291380.19361432157097
2.5196-2.60970.24621390.20311404154397
2.6097-2.71420.3171300.20971426155696
2.7142-2.83770.28591450.22081409155497
2.8377-2.98730.24221450.20451459160498
2.9873-3.17440.27191400.20811459159999
3.1744-3.41940.27731420.19141450159298
3.4194-3.76340.20681450.18031447159299
3.7634-4.30760.20281460.15861465161199
4.3076-5.42580.18271450.158914941639100
5.4258-46.19490.2151420.19581513165599
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)
13.56550.98110.78381.45860.59791.74570.2616-0.68030.50710.5657-0.2969-0.022-0.35340.59780.14260.2731-0.1287-0.0070.3779-0.0770.2135-4.8747-12.57386.6302
20.211-0.03370.07833.8332.78072.06410.9842-0.077-0.27470.4520.04220.07571.65750.1843-0.25271.0786-0.21920.06460.6144-0.28790.6138-26.3816-37.02417.845
36.21063.73361.57712.81032.20375.7127-0.1442-0.0082-0.2872-0.25670.1496-0.0903-0.0906-0.6038-0.05210.1485-0.05430.02280.20080.00910.1399-23.7072-27.82860.138
43.2395-0.28140.37214.5116-0.4643.08160.1588-0.21060.5120.2848-0.02680.0004-0.5886-0.0189-0.02310.24290.00250.06130.1641-0.03520.2437-13.2611-12.5236-3.3137
51.0148-1.53530.81632.3253-1.15431.15720.16020.0504-0.5286-0.1108-0.3285-0.30450.33480.2547-0.45590.37980.13650.01880.30650.14960.4488-5.4528-34.30422.4223
63.0542-1.2268-0.8913.2107-0.74793.4677-0.04340.1489-0.56740.11080.22820.16871.5015-0.2324-0.20620.4055-0.05140.03320.18740.04240.3547-16.6203-36.8003-1.5703
72.2662.58672.39034.96231.57996.21520.0829-0.0976-1.102-0.2066-0.039-0.28050.90480.2867-0.0370.29870.06470.01170.2025-0.01240.2848-5.4506-31.9473-6.1117
85.4313-0.74970.75415.7535-0.79835.7350.29230.23750.5946-0.149-0.4677-0.0935-0.44710.75840.16550.121-0.03490.05420.1567-0.04350.1283-4.6939-14.2733-5.4092
96.4977-1.13761.07080.5187-0.35114.47710.3833-0.17920.71540.1771-0.1987-0.1611-1.13150.92610.23340.0148-0.2116-0.11750.461-0.07610.16216.9742-11.8266-4.2833
103.52040.41570.08792.20610.41132.94280.2915-0.3028-0.4825-0.103-0.1788-0.2080.25170.3636-0.08790.15320.0009-0.02110.23370.01120.1576-1.2852-22.5094-10.6895
116.4082-0.34080.62192.83422.19513.41490.30820.8005-1.3310.6816-0.65640.20690.6727-1.06450.01030.2184-0.2919-0.19160.6175-0.14880.302-24.4232-26.7152-14.0522
126.79752.5019-2.49365.0999-1.06017.15750.2510.330.7722-0.2558-0.340.991-0.5537-0.4309-0.00280.0560.0259-0.10250.26690.0480.2582-26.3944-18.4169-8.6584
137.247-0.98643.07063.10.28344.68710.08890.0446-0.1946-0.1775-0.0075-0.56150.4861.1649-0.00250.30810.05990.07060.74290.03960.363812.2053-21.4257-30.4301
149.3435-2.2798-2.6122.70550.88333.9230.02270.2976-0.90860.4111-0.35310.3962-0.2001-0.029-0.64091.09510.03360.13141.41930.24850.5133-14.1581-10.6858-47.7797
151.30810.3340.22341.8257-0.69770.37980.03690.5214-0.0344-0.73440.30160.55720.2256-1.38430.02020.3972-0.0526-0.07830.8360.08710.2608-14.4494-18.9712-40.2374
165.82292.84751.15034.2150.51787.0336-0.3150.196-0.6268-0.79240.1306-0.76451.18090.5950.13340.38090.06530.09420.37850.00190.32652.2985-26.5002-35.3334
173.96850.5728-0.02722.67941.40642.88720.0627-0.0945-0.5474-0.158-0.3134-0.27140.63520.31640.08450.32980.08590.01570.28390.05150.21880.3582-25.8394-27.255
185.5395-1.8938-5.51414.39881.55276.64560.01241.0666-0.0348-0.6733-0.40460.1794-1.2679-0.77280.15540.35770.0301-0.04070.31580.03940.191-6.1081-7.8491-37.1236
195.5646-0.09160.55425.1837-0.49394.96120.04850.25150.1308-0.36590.19110.5751-0.7379-0.9725-0.14630.44640.1250.02030.46260.09030.2786-13.0587-9.2947-28.7873
204.6525-0.190.88468.1009-0.28285.1703-0.1495-0.13060.15230.15570.1522-0.00520.0740.6830.10940.22810.01380.00490.35320.00810.15044.4309-18.5856-21.969
212.9883.17611.046.82232.51894.6010.07620.08220.00210.1725-0.1084-0.77240.01721.5248-0.45570.2576-0.0691-0.01370.69040.05760.340112.8167-18.1364-14.9574
225.40831.47711.40341.48870.46226.76240.0258-0.18780.3274-0.0783-0.08220.1386-0.5140.15310.07890.23140.00490.01350.20920.00340.1606-2.0508-15.1556-17.2536
231.9632.86992.24335.8452.32084.2726-0.66221.03030.2-0.7264-0.28521.26220.344-1.91290.40450.3776-0.1516-0.08521.068-0.03570.4688-19.1179-24.0513-28.8933
248.5223-1.4191.36654.2685-0.47053.5036-0.3388-0.0835-0.3560.3153-0.12550.88080.3339-1.76670.31380.6335-0.16960.00230.6017-0.12380.5191-13.9637-30.2112-33.5024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 305:329)A305 - 329
2X-RAY DIFFRACTION2(chain A and resid 330:336)A330 - 336
3X-RAY DIFFRACTION3(chain A and resid 337:356)A337 - 356
4X-RAY DIFFRACTION4(chain A and resid 357:394)A357 - 394
5X-RAY DIFFRACTION5(chain A and resid 395:400)A395 - 400
6X-RAY DIFFRACTION6(chain A and resid 401:420)A401 - 420
7X-RAY DIFFRACTION7(chain A and resid 421:439)A421 - 439
8X-RAY DIFFRACTION8(chain A and resid 440:471)A440 - 471
9X-RAY DIFFRACTION9(chain A and resid 472:501)A472 - 501
10X-RAY DIFFRACTION10(chain A and resid 502:518)A502 - 518
11X-RAY DIFFRACTION11(chain A and resid 519:533)A519 - 533
12X-RAY DIFFRACTION12(chain A and resid 534:548)A534 - 548
13X-RAY DIFFRACTION13(chain B and resid 305:329)B305 - 329
14X-RAY DIFFRACTION14(chain B and resid 330:337)B330 - 337
15X-RAY DIFFRACTION15(chain B and resid 338:351)B338 - 351
16X-RAY DIFFRACTION16(chain B and resid 352:363)B352 - 363
17X-RAY DIFFRACTION17(chain B and resid 364:396)B364 - 396
18X-RAY DIFFRACTION18(chain B and resid 397:410)B397 - 410
19X-RAY DIFFRACTION19(chain B and resid 411:435)B411 - 435
20X-RAY DIFFRACTION20(chain B and resid 436:471)B436 - 471
21X-RAY DIFFRACTION21(chain B and resid 472:501)B472 - 501
22X-RAY DIFFRACTION22(chain B and resid 502:519)B502 - 519
23X-RAY DIFFRACTION23(chain B and resid 520:531)B520 - 531
24X-RAY DIFFRACTION24(chain B and resid 532:549)B532 - 549

+
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