[English] 日本語
Yorodumi
- PDB-7alo: Structure of B*27:09/photoRL9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7alo
TitleStructure of B*27:09/photoRL9
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Lymphocyte antigen HLA-B27
  • Vasoactive intestinal polypeptide receptor 1
KeywordsIMMUNE SYSTEM / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX)
Function / homology
Function and homology information


vasoactive intestinal polypeptide receptor activity / G protein-coupled peptide receptor activity / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen ...vasoactive intestinal polypeptide receptor activity / G protein-coupled peptide receptor activity / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / Glucagon-type ligand receptors / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / G alpha (s) signalling events / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / receptor complex / immune response / G protein-coupled receptor signaling pathway / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / positive regulation of cell population proliferation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
GPCR, family 2, vasoactive intestinal peptide receptor 1 / GPCR, family 2, vasoactive intestinal peptide receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site ...GPCR, family 2, vasoactive intestinal peptide receptor 1 / GPCR, family 2, vasoactive intestinal peptide receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lymphocyte antigen HLA-B27 / Vasoactive intestinal polypeptide receptor 1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLoll, B. / Lan, H. / Freund, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)1325/17-1 Germany
German Research Foundation (DFG)TRR186 A21N Germany
CitationJournal: Nat Commun / Year: 2021
Title: Exchange catalysis by tapasin exploits conserved and allele-specific features of MHC-I molecules.
Authors: Lan, H. / Abualrous, E.T. / Sticht, J. / Fernandez, L.M.A. / Werk, T. / Weise, C. / Ballaschk, M. / Schmieder, P. / Loll, B. / Freund, C.
History
DepositionOct 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / reflns / reflns_shell / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _reflns.number_obs / _reflns_shell.number_unique_obs / _struct_ref.db_code / _struct_ref.db_name / _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.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lymphocyte antigen HLA-B27
B: Beta-2-microglobulin
C: Vasoactive intestinal polypeptide receptor 1
D: Lymphocyte antigen HLA-B27
E: Beta-2-microglobulin
F: Vasoactive intestinal polypeptide receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,25323
Polymers94,4096
Non-polymers1,84417
Water9,494527
1
A: Lymphocyte antigen HLA-B27
B: Beta-2-microglobulin
C: Vasoactive intestinal polypeptide receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,17511
Polymers47,2043
Non-polymers9718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-16 kcal/mol
Surface area19240 Å2
MethodPISA
2
D: Lymphocyte antigen HLA-B27
E: Beta-2-microglobulin
F: Vasoactive intestinal polypeptide receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,07712
Polymers47,2043
Non-polymers8739
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-5 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.200, 69.610, 82.540
Angle α, β, γ (deg.)80.240, 88.362, 89.877
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 2 types, 4 molecules ADBE

#1: Protein Lymphocyte antigen HLA-B27 / MHC class I antigen


Mass: 33871.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R7Z5J3
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Vasoactive intestinal polypeptide receptor 1 / VIP-R-1 / Pituitary adenylate cyclase-activating polypeptide type II receptor / PACAP type II ...VIP-R-1 / Pituitary adenylate cyclase-activating polypeptide type II receptor / PACAP type II receptor / PACAP-R-2 / PACAP-R2 / VPAC1


Mass: 1453.719 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: peptide derived from the vasoactive intestinal polypeptide receptor 1 modified at position 8 of the peptide
Source: (synth.) Homo sapiens (human) / References: UniProt: P32241

-
Non-polymers , 6 types, 544 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20% (w/v) polyethylene glycol 3350, and 200 mM KSCN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 89225 / % possible obs: 97.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.52 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.198 / Net I/σ(I): 5.4
Reflection shellResolution: 1.8→1.92 Å / Mean I/σ(I) obs: 1.06 / Num. unique obs: 15619 / CC1/2: 0.45 / Rrim(I) all: 1.619 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660+SVNrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IB5

5ib5


Resolution: 1.8→40.66 Å / SU ML: 0.2669 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.1879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2659 4452 4.99 %
Rwork0.2234 84749 -
obs0.2256 89201 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.24 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6374 0 121 527 7022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00557016
X-RAY DIFFRACTIONf_angle_d1.04379539
X-RAY DIFFRACTIONf_chiral_restr0.0677947
X-RAY DIFFRACTIONf_plane_restr0.00722095
X-RAY DIFFRACTIONf_dihedral_angle_d21.38342654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.39481400.382716X-RAY DIFFRACTION94.01
1.82-1.840.35791480.32082815X-RAY DIFFRACTION96.93
1.84-1.860.35441520.30592835X-RAY DIFFRACTION97.84
1.86-1.890.33141490.29732901X-RAY DIFFRACTION97.63
1.89-1.910.3241490.28272757X-RAY DIFFRACTION97.29
1.91-1.940.30181510.26412877X-RAY DIFFRACTION97.52
1.94-1.970.33311480.26382866X-RAY DIFFRACTION97.73
1.97-20.2781480.24672774X-RAY DIFFRACTION97.63
2-2.030.30911530.24062870X-RAY DIFFRACTION97.45
2.03-2.060.27331490.23482890X-RAY DIFFRACTION97.72
2.06-2.10.28871430.23372770X-RAY DIFFRACTION97.75
2.1-2.130.28721500.23462842X-RAY DIFFRACTION97.02
2.13-2.170.29661450.23092781X-RAY DIFFRACTION94.33
2.17-2.220.25521500.22052788X-RAY DIFFRACTION97.61
2.22-2.270.26631510.20992881X-RAY DIFFRACTION98
2.27-2.320.29611520.20992845X-RAY DIFFRACTION97.88
2.32-2.380.27041520.21332893X-RAY DIFFRACTION97.88
2.38-2.440.27841480.2142793X-RAY DIFFRACTION97.26
2.44-2.510.2731540.20612886X-RAY DIFFRACTION98
2.51-2.60.22461490.20292822X-RAY DIFFRACTION97.99
2.6-2.690.25141470.21272835X-RAY DIFFRACTION97.77
2.69-2.80.26231470.21292778X-RAY DIFFRACTION95.49
2.8-2.920.25461480.21372842X-RAY DIFFRACTION97.17
2.92-3.080.25541510.20762871X-RAY DIFFRACTION98.12
3.08-3.270.21461490.22382826X-RAY DIFFRACTION97.73
3.27-3.520.28571500.22662834X-RAY DIFFRACTION97.45
3.52-3.880.26071440.2072795X-RAY DIFFRACTION96.01
3.88-4.440.22481440.21422752X-RAY DIFFRACTION94.3
4.44-5.590.25871450.2092840X-RAY DIFFRACTION97.52
5.59-40.660.26551460.22522774X-RAY DIFFRACTION95.14
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)
12.502262579-0.03270530837380.6723041141651.92515426951-0.482326224540.877865488052-0.0283944015302-0.115550072038-0.0570514601823-0.0308585415408-0.0172990253325-0.165010247453-0.05711956960350.06756321399590.01270150465870.123319025013-0.01938285182810.03004378549990.1510331244250.01204322490450.244309732968-0.455570181023-4.9182907777127.4252974968
21.860506012590.1645666945960.02259466621662.9766369127-0.5634346654071.273595070480.1107853456790.2540389225410.0525625519103-0.412784382395-0.1480161261820.09553516806950.005868413618270.1330019477140.0008780060367290.2173164020630.000175021847384-0.01015051483890.2183158135990.02577245716880.19054824446-6.159086586692.9202600361313.7740132371
30.7669462827321.12010037229-0.007767805196553.28847276317-0.0791654563883-0.257215071774-0.1470181657580.1298529105890.0221951443084-0.6967395001420.174626290028-0.307167136190.08520636806750.0675741825213-0.01395411678240.399835187955-0.007216846607850.0584524755280.253042426554-0.01756239154640.376414144710.457110478428-34.472435201915.6649890833
43.6351586641-1.42612655429-0.1029032245924.0592250726-1.235789199183.69650368037-0.1408811984660.2161807987380.06803844362530.1244560997120.2879698463210.161604297472-0.0437431408018-0.322990276185-0.1868665396560.120962784219-0.04260531091450.007668069511850.1436064986840.01949101534550.242581625473-12.9077301695-23.35876023427.1027464705
50.71572263854-1.03761023837-0.1375761709633.27068503275-1.268222388751.50150087112-0.2588543314-0.406030670761-0.3823255441980.0645552443875-0.113106365189-0.636458919650.5839647679640.9040829157910.1462444248730.1703809913140.2878892908730.1061960117990.1838782897510.09040024769360.5493527532564.52633523642-39.99285140634.1541477874
62.32719162319-1.548731652590.2154453472665.59392171492-2.92108721123.78985673857-0.03784360845060.001588776631910.04094893748370.340402534299-0.109657151436-0.391624814748-0.1947455956710.1516082821240.1497805083970.2237609597120.01549760394160.00195131203430.172696044825-0.01593251673060.262328220977-3.73843318797-27.644571747531.9354813458
71.79683967717-1.844626284381.168651507838.82029055475-6.245330758286.59660029885-0.128925396144-0.1713744097210.3967125163970.8353038477210.2889305009960.315342838366-0.563692692938-0.276092965687-0.1876168964220.2450645904920.01470011608890.02303419954350.223887012403-0.04431482941780.370112643428-11.2258262535-21.957797958437.0814681721
84.011283430281.14364465546-0.06213688859286.68558245894-0.06825600300864.96960851189-0.163527055039-1.137105144150.2993958862551.280307327740.0170317372223-0.0302502956261-0.143812597984-0.516095083673-0.06425711890780.3076122036230.0782583037965-0.03216004600650.285446077034-0.0240848078770.351346577705-8.95972924289-32.129650223446.3118758562
93.288776003573.78251473813-3.237013462916.37564244498-4.814219088583.76186837209-0.0733932815823-0.6898184000420.1668895263471.23697213013-0.165881144211-0.797065080291-0.3548289630090.5787019117960.2428085459430.5304911854640.0317945726542-0.1647216139660.252617332086-0.01284563489360.361813950439-1.10646437505-23.921550922242.3908372422
101.51777343659-0.559113829321-0.1624740107754.39735253944-3.031329084763.683895546550.0366585038604-0.0429554045408-0.0009876598015060.1187132213680.1214250864470.008304933168760.01217313609910.0483347484160.1206123669160.1528295322060.00612917084323-0.003609698734180.160170693742-0.01128935078340.341462127861-3.65113896178-20.65674251129.7485083388
112.367421274520.03513601441310.1332852203842.50768583688-0.9812631618233.587869416650.00581259869779-0.305526171362-0.5132467717160.1469261018920.3321998179650.6065136722260.378625326638-0.497572541313-0.120246544650.245038911971-0.04140285476970.01818928080430.2688035763010.02338572303250.557346362314-12.7522703032-31.116983019338.2650498237
126.02277553357-1.32223749716-0.5337606065024.578830081550.07282093582154.525271848080.06428930005890.396573070805-0.733121644222-0.5582954663020.440196076484-0.1605473307520.83885255701-0.08385578644150.2051317506370.297010557293-0.08477713332580.04040234403570.1279668092740.09674043127850.22092229728-9.59464723136-37.28109567132.1778463873
135.61050377681-5.78115417924-1.178850333425.906896623871.396145396771.849805640230.5388584024770.07396501223061.50309533049-0.636393765344-0.0896794377876-0.831200816479-0.751421204111-0.329176954592-0.3732249347930.3024311271550.03182388973980.1232817038350.4534192318650.06077905063560.4761182583681.974194558944.4561729663723.979569144
141.99060507575-0.247948414157-0.2506790549561.69829036662-0.4238478629461.16950299366-0.0298310667580.02404562019310.08217833955130.143614931847-0.0262554125483-0.0171660905927-0.003727975770570.05438745375020.05296413739570.1191679482310.0052314882957-0.01556366437770.132824939751-0.02565509189550.188346337993-1.85209013357-42.532482351668.1025376494
15-0.00362809342869-0.961004024353-0.179001818231.94020133325-0.338278075459-0.306761567302-0.225267607648-0.1166196207970.2341459629730.9488116479790.149274982387-0.482334980963-0.1771179540370.08725984135510.009561462907970.5870284570860.0203129670829-0.1799708929760.288141963606-0.06228496761890.5536944136111.04990879267-11.511855659475.9508131574
164.257970235131.675058471030.06886243267734.69529534883-1.268846308134.506614652180.170162496730.173716877607-0.2072204403520.1801181284880.1422713616610.456472189974-0.0508243333543-0.146607047709-0.1182188993320.183005086180.0403500212352-0.03276565498260.1593074387270.02142809469610.351673243403-11.6597823352-20.550095199463.923960017
171.583592956340.134156392896-0.5022946111812.45709969153-1.557799405253.53391646543-0.1399214693640.154537123399-0.108261378380.000997993505570.0768326228354-0.398140996117-0.1342286231780.180725721414-0.03475025861780.163080890075-0.0366743613721-0.02588280705970.190161290554-0.003724527088680.330574134547-4.62566821106-15.864440268255.5838212329
182.081440917651.11486266477-0.625374536724.60793827816-2.727194149084.430996681420.0004828237487090.004519097397840.125851810621-0.337682240357-0.166731041598-0.1743104635990.1306862216080.3556562276740.1327954564430.200644174587-0.01085413416970.0005081612858950.184242105240.0163273671540.346253845145-2.91147357467-24.042102861859.0257122722
192.634157052131.09567920764-0.2670590737242.73335134861-0.5778966897623.451824048570.0399157994260.0918791928340.0927848843529-0.02688767932130.1743407044030.310681112433-0.553266216134-0.317534190078-0.06370374819420.2136270313710.0438672439545-0.02431397610320.2038153337560.07825703115230.410674150269-11.8448917448-12.008147620155.9076160037
207.260466703126.723862978580.2456354714566.180311512450.1051523052372.535112677560.3569917300390.0508764635162-1.527386898930.5572745401630.133928744727-0.7350310951070.635250703297-0.281394339544-0.4137554152190.3279001042510.0150740040325-0.1246718823450.3663999618370.02078801323210.464575660781.92840063692-49.954747733967.5065937187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 276 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 11 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 19 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 30 )
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 41 )
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 46 )
9X-RAY DIFFRACTION9chain 'B' and (resid 47 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 90 )
12X-RAY DIFFRACTION12chain 'B' and (resid 91 through 99 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 9 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 162 )
15X-RAY DIFFRACTION15chain 'D' and (resid 163 through 276 )
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 11 )
17X-RAY DIFFRACTION17chain 'E' and (resid 12 through 46 )
18X-RAY DIFFRACTION18chain 'E' and (resid 47 through 71 )
19X-RAY DIFFRACTION19chain 'E' and (resid 72 through 99 )
20X-RAY DIFFRACTION20chain 'F' and (resid 1 through 9 )

+
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