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- PDB-5nj8: Structural basis for aryl hydrocarbon receptor mediated gene acti... -

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Basic information

Entry
Database: PDB / ID: 5nj8
TitleStructural basis for aryl hydrocarbon receptor mediated gene activation
Components
  • (Aryl hydrocarbon ...) x 2
  • DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*CP*AP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*TP*GP*CP*GP*TP*GP*AP*CP*C)-3')
KeywordsTRANSCRIPTION / basic helix loop helix PAS domain transcription factor
Function / homology
Function and homology information


negative regulation of T cell mediated immune response to tumor cell / cytosolic aryl hydrocarbon receptor complex / regulation of B cell proliferation / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / cellular response to molecule of bacterial origin / regulation of adaptive immune response / Regulation of gene expression by Hypoxia-inducible Factor ...negative regulation of T cell mediated immune response to tumor cell / cytosolic aryl hydrocarbon receptor complex / regulation of B cell proliferation / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / cellular response to molecule of bacterial origin / regulation of adaptive immune response / Regulation of gene expression by Hypoxia-inducible Factor / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / positive regulation of protein sumoylation / Xenobiotics / Phase I - Functionalization of compounds / positive regulation of vascular endothelial growth factor receptor signaling pathway / Regulation of gene expression by Hypoxia-inducible Factor / blood vessel development / E-box binding / aryl hydrocarbon receptor binding / TFIID-class transcription factor complex binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / Endogenous sterols / cis-regulatory region sequence-specific DNA binding / cellular response to cAMP / cellular response to forskolin / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / TBP-class protein binding / positive regulation of glycolytic process / xenobiotic metabolic process / cAMP-mediated signaling / positive regulation of erythrocyte differentiation / circadian regulation of gene expression / Hsp90 protein binding / PPARA activates gene expression / response to toxic substance / transcription coactivator binding / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / regulation of gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / nuclear body / transcription cis-regulatory region binding / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / cell cycle / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / protein-containing complex binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / Nuclear translocator / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Helix-loop-helix DNA-binding domain superfamily ...Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / Nuclear translocator / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / 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
Similarity search - Domain/homology
ACETATE ION / ERBIUM (III) ION / DNA / DNA (> 10) / Aryl hydrocarbon receptor nuclear translocator / Aryl hydrocarbon receptor / Aryl hydrocarbon receptor nuclear translocator
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsDaumke, O. / Schulte, K.W.
CitationJournal: Structure / Year: 2017
Title: Structural Basis for Aryl Hydrocarbon Receptor-Mediated Gene Activation.
Authors: Schulte, K.W. / Green, E. / Wilz, A. / Platten, M. / Daumke, O.
History
DepositionMar 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Feb 5, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_asym.entity_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor
B: Aryl hydrocarbon receptor nuclear translocator
C: Aryl hydrocarbon receptor
D: Aryl hydrocarbon receptor nuclear translocator
E: DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*CP*AP*AP*CP*C)-3')
F: DNA (5'-D(*GP*GP*TP*TP*GP*CP*GP*TP*GP*AP*CP*C)-3')
G: DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*CP*AP*AP*CP*C)-3')
H: DNA (5'-D(*GP*GP*TP*TP*GP*CP*GP*TP*GP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,50121
Polymers124,4358
Non-polymers2,06613
Water00
1
A: Aryl hydrocarbon receptor
B: Aryl hydrocarbon receptor nuclear translocator
E: DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*CP*AP*AP*CP*C)-3')
F: DNA (5'-D(*GP*GP*TP*TP*GP*CP*GP*TP*GP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,44712
Polymers62,2174
Non-polymers1,2308
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-114 kcal/mol
Surface area21180 Å2
MethodPISA
2
C: Aryl hydrocarbon receptor
D: Aryl hydrocarbon receptor nuclear translocator
G: DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*CP*AP*AP*CP*C)-3')
H: DNA (5'-D(*GP*GP*TP*TP*GP*CP*GP*TP*GP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0549
Polymers62,2174
Non-polymers8365
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-109 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.321, 91.321, 464.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11H-101-

ER3

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Components

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Aryl hydrocarbon ... , 2 types, 4 molecules ACBD

#1: Protein Aryl hydrocarbon receptor / AhR / Class E basic helix-loop-helix protein 76 / bHLHe76


Mass: 28423.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AHR, BHLHE76 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosette / References: UniProt: P35869
#2: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF1-beta


Mass: 26467.090 Da / Num. of mol.: 2 / Mutation: C256S
Source method: isolated from a genetically manipulated source
Details: internal deletion of 274-301 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt / Production host: Escherichia coli (E. coli) / References: UniProt: P53762, UniProt: P27540*PLUS

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DNA chain , 2 types, 4 molecules EGFH

#3: DNA chain DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*CP*AP*AP*CP*C)-3')


Mass: 3632.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Dioxin response element / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(*GP*GP*TP*TP*GP*CP*GP*TP*GP*AP*CP*C)-3')


Mass: 3694.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Dioxin response element / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 13 molecules

#5: Chemical
ChemComp-ER3 / ERBIUM (III) ION


Mass: 167.259 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Er
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2

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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: 2 Å3/Da / Density % sol: 39 % / Description: Plates
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 10 mM HEPES/NaOH pH 6.8, 18% PEG3350, 200 mM ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.476 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 28, 2015 / Details: MIRRORS
RadiationMonochromator: Si111-DCM with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.476 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 32653 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 18 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rsym value: 0.098 / Net I/σ(I): 7.82
Reflection shellResolution: 3.3→3.49 Å / Redundancy: 16.5 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 4.11 / Num. unique obs: 5197 / CC1/2: 0.979 / Rsym value: 0.683 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→46.83 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 35.16
RfactorNum. reflection% reflection
Rfree0.3327 917 5 %
Rwork0.2921 --
obs0.2942 18323 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 968 16 0 5848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056042
X-RAY DIFFRACTIONf_angle_d0.6788337
X-RAY DIFFRACTIONf_dihedral_angle_d16.8883448
X-RAY DIFFRACTIONf_chiral_restr0.042981
X-RAY DIFFRACTIONf_plane_restr0.004908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.4740.41471240.31632352X-RAY DIFFRACTION98
3.474-3.69160.36211250.32462385X-RAY DIFFRACTION98
3.6916-3.97650.39851300.31842451X-RAY DIFFRACTION100
3.9765-4.37640.33531290.2852452X-RAY DIFFRACTION100
4.3764-5.00910.33251300.27152479X-RAY DIFFRACTION100
5.0091-6.30850.33181340.2992536X-RAY DIFFRACTION100
6.3085-46.83510.29521450.28212751X-RAY DIFFRACTION100
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)
10.2699-0.0621-0.04380.92390.19880.0466-0.2327-0.06690.1527-0.1365-0.0351-0.3148-0.08710.0586-0.06231.48330.1718-0.08320.4494-0.01470.3373-0.512429.3907200.4939
20.2473-0.12430.09110.05540.00430.1466-0.2861-0.01-0.1566-0.07850.00420.3563-0.12540.15460.00321.28290.2819-0.16930.5549-0.05730.8809-9.933221.964200.0559
30.00310.02050.04670.18330.3670.8193-0.18270.0220.0576-0.0635-0.2832-0.3442-0.1078-0.0914-0.18620.35510.0903-0.01510.2080.09480.665314.937124.7156229.6474
4-0.01960.039-0.00360.211-0.11240.10160.0882-0.07310.1305-0.1875-0.334-0.23630.16210.0418-0.04250.3010.0017-0.04360.26920.09160.328314.608915.012232.6177
5-0.00050.0108-0.00090.00270.0028-0.0014-0.0539-0.1525-0.2233-0.38160.2069-0.04850.13150.08850.00011.42490.1182-0.22590.7188-0.13320.6163-8.19039.9676197.5579
60.09570.12930.01630.14350.00530.08790.17130.4695-0.61420.00720.5784-0.3336-0.0675-0.2281-0.00071.5450.0689-0.25870.8069-0.08370.6398-7.42279.7617198.6716
70.1755-0.0410.22770.47860.14080.3410.5140.18670.25410.27650.0035-0.1642-0.1716-0.29540.73270.7124-0.00060.13930.53250.20540.33541.938911.0616237.1803
80.02930.0017-0.02730.06610.00180.02250.00170.21870.13120.407-0.01280.0605-0.1287-0.3221-0.00010.8036-0.0360.00710.63940.07970.59581.005211.643236.3805
90.1233-0.13510.19550.1297-0.17650.27790.3959-0.0544-0.01690.10190.1504-0.0312-0.02170.01570.79880.47310.386-0.0991-0.2680.3090.1554-9.056942.1127218.9071
100.19610.16190.05150.0915-0.01890.1288-0.0585-0.02240.0896-0.11990.07650.2342-0.09430.08210.1120.5575-0.00140.1528-0.0410.01920.52965.015460.0065220.069
110.033-0.0677-0.02830.15290.04420.0217-0.0365-0.01160.16120.0323-0.1037-0.1770.19630.0377-0.31970.79180.32210.72030.2526-0.0830.33127.514819.56211.2753
120.06870.03770.03340.03220.01840.02240.2249-0.2769-0.10540.00950.0376-0.38180.0816-0.35890.21990.5686-0.05580.56460.38760.26610.728234.744936.0055207.789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 34 through 88)
2X-RAY DIFFRACTION2(chain 'B' and resid 85 through 143)
3X-RAY DIFFRACTION3(chain 'C' and resid 32 through 88)
4X-RAY DIFFRACTION4(chain 'D' and resid 84 through 144)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 12)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 12)
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 12)
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 12)
9X-RAY DIFFRACTION9(chain 'A' and resid 109 through 272)
10X-RAY DIFFRACTION10(chain 'B' and resid 152 through 345)
11X-RAY DIFFRACTION11(chain 'C' and resid 107 through 271)
12X-RAY DIFFRACTION12(chain 'D' and resid 148 through 342)

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  • 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

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