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- PDB-2gpv: Estrogen Related Receptor-gamma ligand binding domain complexed w... -

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Basic information

Entry
Database: PDB / ID: 2gpv
TitleEstrogen Related Receptor-gamma ligand binding domain complexed with 4-hydroxy-tamoxifen and a SMRT peptide
Components
  • Estrogen-related receptor gamma
  • Nuclear receptor corepressor 2
KeywordsTRANSCRIPTION / Estrogen related receptor / ERR / ERRg / ESRRG / Nuclear Receptor / Steroid Receptor / SMRT / Tamoxifen
Function / homology
Function and homology information


AF-2 domain binding / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / Notch binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity ...AF-2 domain binding / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / Notch binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity / estrous cycle / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to organonitrogen compound / lactation / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / steroid binding / cerebellum development / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Nuclear Receptor transcription pathway / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / response to estradiol / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus
Similarity search - Function
Oestrogen-related receptor / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Retinoic acid receptor / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / Estrogen receptor/oestrogen-related receptor / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...Oestrogen-related receptor / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Retinoic acid receptor / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / Estrogen receptor/oestrogen-related receptor / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Retinoid X Receptor / Retinoid X Receptor / Homeobox-like domain superfamily / 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
4-HYDROXYTAMOXIFEN / Estrogen-related receptor gamma / Chromosome undetermined SCAF24640, whole genome shotgun sequence / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWang, L. / Zuercher, W.J. / Consler, T.G. / Lambert, M.H. / Miller, A.B. / Osband-miller, L.A. / McKee, D.D. / Willson, T.M. / Nolte, R.T.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: X-ray crystal structures of the estrogen-related receptor-gamma ligand binding domain in three functional states reveal the molecular basis of small molecule regulation.
Authors: Wang, L. / Zuercher, W.J. / Consler, T.G. / Lambert, M.H. / Miller, A.B. / Orband-Miller, L.A. / McKee, D.D. / Willson, T.M. / Nolte, R.T.
History
DepositionApr 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 22, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.5Aug 30, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen-related receptor gamma
B: Estrogen-related receptor gamma
C: Estrogen-related receptor gamma
D: Estrogen-related receptor gamma
E: Estrogen-related receptor gamma
F: Estrogen-related receptor gamma
G: Nuclear receptor corepressor 2
H: Nuclear receptor corepressor 2
I: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,63115
Polymers164,3069
Non-polymers2,3256
Water1,09961
1
A: Estrogen-related receptor gamma
B: Estrogen-related receptor gamma
D: Estrogen-related receptor gamma
E: Estrogen-related receptor gamma
G: Nuclear receptor corepressor 2
H: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,08810
Polymers109,5376
Non-polymers1,5504
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14310 Å2
ΔGint-71 kcal/mol
Surface area39460 Å2
MethodPISA
2
C: Estrogen-related receptor gamma
F: Estrogen-related receptor gamma
I: Nuclear receptor corepressor 2
hetero molecules

C: Estrogen-related receptor gamma
F: Estrogen-related receptor gamma
I: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,08810
Polymers109,5376
Non-polymers1,5504
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area14360 Å2
ΔGint-63 kcal/mol
Surface area39460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.22, 117.17, 90.47
Angle α, β, γ (deg.)90, 102.36, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-42-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
13G
23H
33I

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSILEILEAA232 - 4384 - 210
21PROPROILEILEBB233 - 4385 - 210
31PROPROILEILECC233 - 4385 - 210
41PROPROILEILEDD233 - 4385 - 210
51TYRTYRILEILEEE234 - 4386 - 210
61PROPROILEILEFF233 - 4385 - 210
12LYSLYSGLUGLUAA439 - 455211 - 227
22LYSLYSGLUGLUBB439 - 455211 - 227
32LYSLYSGLUGLUCC439 - 455211 - 227
13GLYGLYGLYGLYGG1319 - 13304 - 15
23GLYGLYGLYGLYHH1319 - 13304 - 15
33GLYGLYGLYGLYII1319 - 13304 - 15

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Estrogen-related receptor gamma / / Estrogen receptor-related protein 3 / ERR gamma-2


Mass: 26084.373 Da / Num. of mol.: 6 / Fragment: Ligand Binding Domain (residues 229-458)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRG / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62508
#2: Protein/peptide Nuclear receptor corepressor 2 / N-CoR2 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRT / SMRTe / Thyroid- ...N-CoR2 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRT / SMRTe / Thyroid- / retinoic-acid-receptor-associated corepressor / T3 receptor- associating factor / TRAC / CTG repeat protein 26 / SMAP270 /


Mass: 2599.999 Da / Num. of mol.: 3 / Fragment: LXXLL Motif (residues 2338-2359) / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: Q9Y618, UniProt: Q4RA23*PLUS
#3: Chemical
ChemComp-OHT / 4-HYDROXYTAMOXIFEN / Afimoxifene


Mass: 387.514 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H29NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 7% PEG3350 0.2M Lithium Acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 48079 / Num. obs: 43368 / % possible obs: 90.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.093 / Χ2: 1.018
Reflection shellResolution: 2.85→2.95 Å / % possible obs: 39.9 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.298 / Num. measured obs: 1891 / Χ2: 0.86 / % possible all: 38.21

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT1.7data extraction
MAR345data collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GP7
Resolution: 2.85→19.91 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.819 / SU B: 34.341 / SU ML: 0.319 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1359 3.1 %RANDOM
Rwork0.219 ---
all0.221 47597 --
obs0.221 43251 90.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.974 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å2-0.55 Å2
2--0.14 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10545 0 174 61 10780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210995
X-RAY DIFFRACTIONr_bond_other_d0.0010.027335
X-RAY DIFFRACTIONr_angle_refined_deg1.1642.00614878
X-RAY DIFFRACTIONr_angle_other_deg0.863318121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15551340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38525.804460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.053152066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9661533
X-RAY DIFFRACTIONr_chiral_restr0.0560.21716
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022049
X-RAY DIFFRACTIONr_nbd_refined0.2310.22846
X-RAY DIFFRACTIONr_nbd_other0.180.27227
X-RAY DIFFRACTIONr_nbtor_refined0.1830.25449
X-RAY DIFFRACTIONr_nbtor_other0.0860.25602
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2257
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.22
X-RAY DIFFRACTIONr_mcbond_it0.3351.57033
X-RAY DIFFRACTIONr_mcbond_other0.0681.52678
X-RAY DIFFRACTIONr_mcangle_it0.536210833
X-RAY DIFFRACTIONr_scbond_it0.8334638
X-RAY DIFFRACTIONr_scangle_it1.2974.54045
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberRmsTypeWeight
11A11920.19MEDIUM POSITIONAL0.5
12B11920.19MEDIUM POSITIONAL0.5
13C11920.18MEDIUM POSITIONAL0.5
14D11920.2MEDIUM POSITIONAL0.5
15E11920.2MEDIUM POSITIONAL0.5
16F11920.2MEDIUM POSITIONAL0.5
11A14630.57LOOSE POSITIONAL5
12B14630.59LOOSE POSITIONAL5
13C14630.53LOOSE POSITIONAL5
14D14630.78LOOSE POSITIONAL5
15E14630.55LOOSE POSITIONAL5
16F14630.56LOOSE POSITIONAL5
11A11920.32MEDIUM THERMAL2
12B11920.27MEDIUM THERMAL2
13C11920.27MEDIUM THERMAL2
14D11920.27MEDIUM THERMAL2
15E11920.3MEDIUM THERMAL2
16F11920.32MEDIUM THERMAL2
11A14630.89LOOSE THERMAL10
12B14630.85LOOSE THERMAL10
13C14630.88LOOSE THERMAL10
14D14630.8LOOSE THERMAL10
15E14630.78LOOSE THERMAL10
16F14630.93LOOSE THERMAL10
21A940.35MEDIUM POSITIONAL0.5
22B940.32MEDIUM POSITIONAL0.5
23C940.32MEDIUM POSITIONAL0.5
21A1300.9LOOSE POSITIONAL5
22B1300.86LOOSE POSITIONAL5
23C1300.73LOOSE POSITIONAL5
21A940.25MEDIUM THERMAL2
22B940.2MEDIUM THERMAL2
23C940.2MEDIUM THERMAL2
21A1300.58LOOSE THERMAL10
22B1300.47LOOSE THERMAL10
23C1300.49LOOSE THERMAL10
31G630.51MEDIUM POSITIONAL0.5
32H630.31MEDIUM POSITIONAL0.5
33I630.37MEDIUM POSITIONAL0.5
31G660.99LOOSE POSITIONAL5
32H660.91LOOSE POSITIONAL5
33I660.81LOOSE POSITIONAL5
31G630.17MEDIUM THERMAL2
32H630.25MEDIUM THERMAL2
33I630.25MEDIUM THERMAL2
31G660.96LOOSE THERMAL10
32H660.99LOOSE THERMAL10
33I660.6LOOSE THERMAL10
LS refinement shellResolution: 2.85→2.922 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 40 -
Rwork0.299 1272 -
all-1312 -
obs--38.21 %
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)
11.12990.40650.05082.9640.91844.28170.1058-0.10820.06590.2227-0.12720.1168-0.19780.00310.0214-0.14910.02840.0927-0.26710.0261-0.141738.5290.94943.962
21.6328-1.061-1.07715.07171.20653.976-0.03840.145-0.1079-0.1703-0.14460.14610.44020.03240.1829-0.06950.08020.109-0.22780.0268-0.12328.379-16.92387.165
34.0818-0.6747-1.14291.72290.64444.53010.0145-0.1792-0.03740.0940.0520.0562-0.2576-0.5111-0.0664-0.17790.0746-0.0264-0.11670.019-0.094467.056-17.736109.052
40.8674-0.17130.03143.92460.72883.2174-0.1523-0.1122-0.13660.2104-0.08940.58840.4333-0.45520.2418-0.017-0.03160.1386-0.13210.0167-0.027226.162-20.4943.048
51.9945-1.03310.66782.3765-1.09262.52390.13670.2270.0078-0.1592-0.11930.2025-0.2637-0.0824-0.0174-0.04260.0620.112-0.2112-0.0329-0.129820.1445.70588.841
61.5898-0.13151.16270.4282-0.23032.5552-0.0129-0.1041-0.16060.05020.0025-0.05910.09820.36760.0104-0.1240.06510.0722-0.1149-0.01110.009786.417-29.24109.651
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA232 - 4394 - 211
21GG1319 - 13304 - 15
32BB233 - 4395 - 211
42HH1319 - 13304 - 15
53CC233 - 4395 - 211
63II1319 - 13304 - 15
74DD233 - 4415 - 213
84AA440 - 455212 - 227
95EE234 - 4416 - 213
105CC440 - 455212 - 227
116FF233 - 4405 - 212
126BB440 - 455212 - 227

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