[English] 日本語
Yorodumi
- PDB-7lfk: MODEL OF MHC CLASS Ib H2-M3 WITH MOUSE ND1 N-TERMINAL HEPTAPEPTID... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lfk
TitleMODEL OF MHC CLASS Ib H2-M3 WITH MOUSE ND1 N-TERMINAL HEPTAPEPTIDE, THR MUTANT, REFINED AT 1.60 ANGSTROMS RESOLUTION
Components
  • Beta-2-microglobulin
  • Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
  • Histocompatibility 2, M region locus 3
KeywordsIMMUNE SYSTEM / HISTOCOMPATIBILITY ANTIGEN/PEPTIDE / HISTOCOMPATIBILITY ANTIGEN-PEPTIDE COMPLEX
Function / homology
Function and homology information


alpha-beta T cell activation involved in immune response / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / Complex I biogenesis / Respiratory electron transport / positive regulation of natural killer cell mediated cytotoxicity / response to hydroperoxide / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...alpha-beta T cell activation involved in immune response / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / Complex I biogenesis / Respiratory electron transport / positive regulation of natural killer cell mediated cytotoxicity / response to hydroperoxide / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / cellular defense response / nitric oxide biosynthetic process / aerobic respiration / Neutrophil degranulation / 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 / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / response to organic cyclic compound / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / 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 / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / 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 / positive regulation of immune response / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / mitochondrial inner membrane / learning or memory / response to hypoxia / defense response to bacterium / response to xenobiotic stimulus / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / neuronal cell body / dendrite / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / cytosol
Similarity search - Function
NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / 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 ...NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / 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
Beta-2-microglobulin / NADH-ubiquinone oxidoreductase chain 1 / Histocompatibility 2, M region locus 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsTomchick, D.R. / Deisenhofer, J. / Shen, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM079383 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-DA035778 United States
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 2022
Title: Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides.
Authors: Strand, A. / Shen, S.T. / Tomchick, D.R. / Wang, J. / Wang, C.R. / Deisenhofer, J.
#1: Journal: Cell / Year: 1995
Title: Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3
Authors: Wang, C.R. / Castano, A.R. / Peterson, P.A. / Slaughter, C. / Lindahl, K.F. / Deisenhofer, J.
#2: Journal: Cell / Year: 1991
Title: H2-M3 encodes the MHC Class I molecule presenting the maternally transmitted antigen of the mouse
Authors: Wang, C.R. / Loveland, B.E. / Lindahl, K.F.
History
DepositionJan 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histocompatibility 2, M region locus 3
B: Beta-2-microglobulin
C: Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
D: Histocompatibility 2, M region locus 3
E: Beta-2-microglobulin
F: Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,89513
Polymers90,5366
Non-polymers3597
Water8,305461
1
A: Histocompatibility 2, M region locus 3
B: Beta-2-microglobulin
C: Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5587
Polymers45,2683
Non-polymers2904
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-56 kcal/mol
Surface area19630 Å2
MethodPISA
2
D: Histocompatibility 2, M region locus 3
E: Beta-2-microglobulin
F: Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3376
Polymers45,2683
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-46 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.430, 69.100, 54.800
Angle α, β, γ (deg.)102.537, 93.860, 114.100
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 Histocompatibility 2, M region locus 3 / MHC Class Ib Antigen H2-M3 / MHC class I antigen H-2M3


Mass: 32650.650 Da / Num. of mol.: 2 / Mutation: G299 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-M3, H-2M3 / Plasmid: pRMHa-3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q31093
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pRMHa-3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887

-
Protein/peptide / Sugars , 2 types, 3 molecules CF

#3: Protein/peptide Heptapeptide from NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 913.091 Da / Num. of mol.: 2 / Fragment: First seven amino-terminal residues / Mutation: I6T / Source method: obtained synthetically / Details: The N-terminal methionine is N-Formylmethionine / Source: (synth.) Mus musculus (house mouse)
References: UniProt: P03888, NADH:ubiquinone reductase (H+-translocating)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 467 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes, 20% (w/v) PEG 4000, 30% (v/v) ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jan 4, 1999 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.6→31.7 Å / Num. obs: 93324 / % possible obs: 86.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.13 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.6
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5139 / % possible all: 68

-
Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.27data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1MHC

1mhc


Resolution: 1.6→31.62 Å / SU ML: 0.1955 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.252
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 2001 2.14 %
Rwork0.2082 91318 -
obs0.209 93319 86.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.67 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 20 461 6717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01816446
X-RAY DIFFRACTIONf_angle_d1.43538749
X-RAY DIFFRACTIONf_chiral_restr0.0866915
X-RAY DIFFRACTIONf_plane_restr0.01151135
X-RAY DIFFRACTIONf_dihedral_angle_d18.53832416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.27611170.23395139X-RAY DIFFRACTION68.1
1.64-1.680.29381360.24396218X-RAY DIFFRACTION82.59
1.68-1.730.30561440.2436363X-RAY DIFFRACTION84.73
1.73-1.790.29951360.24126341X-RAY DIFFRACTION84.39
1.79-1.850.29711450.23366198X-RAY DIFFRACTION82.06
1.85-1.930.25991380.23266335X-RAY DIFFRACTION84.35
1.93-2.020.26551340.21466579X-RAY DIFFRACTION86.89
2.02-2.120.26381400.2036645X-RAY DIFFRACTION88.06
2.12-2.250.23711460.20366737X-RAY DIFFRACTION89.67
2.25-2.430.26781570.20936878X-RAY DIFFRACTION91.46
2.43-2.670.28191490.21257043X-RAY DIFFRACTION93.57
2.67-3.060.22271500.20887121X-RAY DIFFRACTION94.54
3.06-3.850.22521560.20076852X-RAY DIFFRACTION90.91
3.85-31.620.2121530.19316869X-RAY DIFFRACTION91.24
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)
13.69567558043-1.20200648341-0.8125660223463.42703950318-0.1355038863543.22776681217-0.112814554991-0.2577589804960.1601559356960.208582443773-0.00758325557045-0.164053598343-0.1660900100590.3928735584930.06168685186760.17317805129-0.0263232976354-0.02220869646040.1903255593010.0112260487250.086555239265137.326491500321.971799541720.0039557787
27.77396069992-1.65899168368-2.092824772222.649621183980.5380959751991.658711852450.3117131197910.4196046903360.8939847139780.0148262479274-0.21377652764-0.149640889496-0.4892739078840.00937017180197-0.1086847057430.324946444169-0.0379194173685-0.04646077024390.1555091268290.04084417373890.1650542027931.119549411532.721218066716.6753235327
33.207148861110.297027238471-0.0011082933742.86355730568-0.5133635618982.85655659397-0.02053560802380.0800374697181-0.00817425800174-0.1188685682860.02051828036590.1241998710480.04956143589440.11808604053-0.005525529084260.09605139185750.012571240604-0.02249934949580.118913362281-0.007699489566080.088828555902424.878416949420.466558920612.9627491273
45.190750498481.06892137437-2.488770851760.699559609708-0.5540720021354.25285195807-0.007305808771910.4643607253480.198007254174-0.205534392020.05376209660610.189052630951-0.143261983631-0.0634600511231-0.03931225125380.1939612455040.00633605540481-0.04877023915140.138812052891-0.008997946749350.14934354698119.371452208424.37097454475.76250907896
50.8630649995520.675530854463-0.6637489791624.82877849508-2.963193867232.68420280922-0.140294065942-0.0555001815769-0.222184486045-0.484075823038-0.175711621243-0.2402642711220.5128218490480.3092830734420.285217880880.272426654620.09577724704870.04803048996830.245644818617-0.02551851980310.17677311052736.3382368341-2.1330265808619.7960632618
63.41811147211.28668147676-0.3932601708854.26192634257-1.704177929243.05925533360.03832190455620.0696176087542-0.143839592292-0.390301596821-0.03581832816580.421247767050.446246626257-0.169121701997-0.02316353996520.2212686773680.06448386976270.0022052801370.169400770339-0.05010606232190.20030017563727.3898735927-7.251172643125.7437937994
72.620287189920.294980253447-0.8408732545280.251463460033-0.3850621357872.29898314855-0.2436110105940.086157610749-0.802136566011-0.645030778768-0.0321334785049-0.2942477644110.9354989091970.001639382103290.2229232412860.6057418983410.05736722029220.08883892262590.222119569867-0.0478596835690.44127080550431.2383711566-17.170825650921.6105753404
88.3769588779-6.099159215913.665560843628.23729530638-3.062132382747.331687097510.2339977084980.242421943219-0.274086660206-0.219349019185-0.2194527921710.6148078264020.0521607702628-0.414473039162-0.0825549773910.130023392956-0.02929148815990.01181816999260.196813770257-0.03555136619280.14072625130625.61074352327.8978700598232.198443727
93.77442362383-0.01285530933531.07264383264.27375320186-1.92487403613.236388129560.1555857018220.225798819518-0.580669655902-0.0116621306725-0.420540761517-1.052183829470.8645130530971.201810846170.2686248691170.3749169741170.19603613040.005355385690470.439728918140.03367555217250.34756822297245.4452849213-4.0322094373835.2385297098
108.1002011286-6.889074810461.4099808857.88118831312-2.045096379252.422433190680.106869279792-0.0804719666276-0.0142969044672-0.200059474573-0.173185169867-0.1553045380090.1913587889990.2317485690770.04728796360490.1130374440110.003890282487110.03221501335880.1739383429320.00245315257770.09636760050534.49163554696.6015264689732.3308310983
119.41141307753-7.889267487048.625185652987.80234401881-7.235621705198.2847030326-0.358167732875-0.01684428752040.009070427109040.3798028102950.126737204878-0.110640823515-0.6506599685830.05052188863950.1926325331930.1641386448230.03414065261430.03057228743310.2758018384570.01515808530780.14464542718630.248299340514.980743555837.4951697415
122.119580963271.19739517648-1.930359131655.69913906675-5.277495834517.396737799860.06546356135340.01051697688680.1199328170460.375321536645-0.423430976048-0.705611265127-0.7446633560791.557842966290.3298846728870.295263485286-0.123980904334-0.05199695388610.4513246921920.04416341071960.28579367199840.802094133212.001380092542.6129607838
135.48449027471-3.551351602583.656990454093.99816799591-3.469068736884.657104726910.2529972662950.0472715136346-0.109349649433-0.211180440004-0.165151150974-0.01424251919070.2488172413440.357611774654-0.08267782734340.1644980559990.007939181021520.04265696869850.216641145189-0.008211441967720.09947081744832.826333988111.842711884527.7630314417
142.33435428338-0.4148304915550.4067293502270.7426150920350.7993477037132.0477421816-0.279867389751-0.672603952973-0.03878146645470.337030167540.2779246532680.04018577269490.207708535018-0.119294269987-0.0138174861240.2100690847610.04147191838260.059018591390.3028739623820.01088539070840.12211543707831.05040830157.3187319630842.9969962443
155.12035181308-4.38431967501-6.394641495618.148877024627.347525429729.21096639385-0.1171743479380.128939259438-0.3230654361620.51470716308-0.2149500921090.08447373673140.5973169961670.1508417947530.3328757541860.2370081567990.007938329668390.0067020370530.2396947666360.03643475918230.16270969222832.3626804942-1.1974587045440.4204235479
169.26297483907-7.49206009252-1.412001967168.936069661680.4617293253826.272229246320.5658700485570.1555978362411.17967720242-0.528212564383-0.03038540831591.48699265199-0.399408712434-0.0321423777336-0.2242741683110.386527139203-0.00189557748504-0.03078015615460.2627452473570.03860572251170.63935418954723.732138927630.106759292311.0130932458
173.33800402560.3960889778760.668185997363.433310941430.2588088031172.61402897941-0.1406553578010.376768180814-0.0821655469558-0.1194622271390.0495121689635-0.251851291593-0.003007529082950.3429373753820.0787195369580.192590661571-0.0407339781031-0.02504888519050.182628305870.0392401396160.1403726385947.17243455301-13.21266748932.57938013057
187.844759938251.678910372913.887451777222.426643600980.456991596013.567882406510.4432230865160.0726617919428-0.7135307875630.13842982769-0.13044792638-0.2115788306760.685572778005-0.017881586435-0.3083237420760.324887833673-0.02511646524170.0423110998290.128555018817-0.01218472815990.1615940401370.291363904418-23.61823101614.10664047792
192.42096414214-0.2423431933370.7558056178790.651618419898-0.6995967136481.55417646432-0.1296237815630.04114352705960.1380541770560.141083706045-0.04162864391770.00345792236462-0.236186368814-0.01688687567540.164691684280.202159980765-0.0366732224512-0.01788851706650.103763265461-0.007001444680810.149607411429-9.4122748022-11.1067355797.60930782178
207.251687124390.1610633757122.915111992372.53475605551-0.09335286044554.63397779169-0.0373439534535-0.313828187556-0.4305057207250.470221472265-0.02272300104320.149028811259-0.175164101677-0.2636923839560.05219762227410.242362074714-0.0241495061750.04709648512840.151391503766-0.01921573709360.145477799382-12.7466209228-17.969408544114.7267517125
211.334834404740.3492125011960.2547415441173.73088488393-1.056563648863.05222806742-0.1122922606540.1216589162850.281264223856-0.08147484103290.07298878049290.218844066565-0.315628190521-0.3498271169370.036487127660.22226470726-0.0479209445806-0.1062526892530.249440529890.008164078721480.2784991003813.2411779533712.74673723732.07301663167
225.44945421525-3.58207429592.870806863244.35519661284-4.790669903638.85470838431-0.07728837502940.2206855290330.608981280659-0.267451937711-0.1003516580130.515464603053-0.801377234481-0.3478371019120.0625732818520.393195746932-0.000165741401844-0.15655149470.2237280944790.000755183127780.4907508615820.61625071188526.13123090622.85872933527
236.823316725546.63716456158-0.6194464656518.926122046410.5014816843713.975678828080.1294398565450.0676136684372-0.04205247832-0.005381601343190.06978800340810.4507437333210.111584974863-0.696871680423-0.1703711222950.246499378865-0.0490667783612-0.112434008140.299652301820.1001768635110.282603584179-2.207972632841.96936251074-11.2549128345
246.370734140044.27148904074-2.062068684375.02656993857-2.189008736614.573139395190.355484246796-0.3539718471410.1927504577680.287425240705-0.340008846067-0.21990414231-0.401577727180.605705198894-0.003400924331820.212433910782-0.0560354632709-0.04541952677740.185053955090.01811958611360.22436849024311.41071665157.8851551056-9.86138062207
259.153418970357.85243347578-8.491063527897.08432575023-7.627216900468.5217431588-0.824230674030.342462599916-0.665822336461-0.957399163590.233778862302-0.719845155850.979652057693-0.1883954618410.5444485751010.502662916286-0.074975140622-0.02522873512410.2538647380640.02216436440660.2904106893713.33052931695-4.67392962179-15.7976909679
263.387635154212.78237579653-2.622659560839.607049778891.175567806973.54221441401-0.3267080366650.103873345631-0.247810792827-1.282464439880.484948954348-0.1918026608261.760127063170.364056443321-0.2536843659940.5514006101630.0106141001991-0.02088249125250.3272225139310.07305741722390.39971510819314.3670064601-1.31422767913-19.1643530276
276.023833094434.07896128513-3.982883406774.51065167161-3.475445925095.293442799890.507285166883-0.3237561921720.2171904329370.274780618848-0.323201959378-0.0269803493262-0.1267922714860.319214619064-0.1439227634910.23659293742-0.0556670538946-0.07637332471280.1528303663310.006836807874620.1559217500314.49035618047-2.32280548302-5.69845405375
284.352416664463.023750523831.47274078983.443213543282.391332412462.50690771815-0.8998158437170.896219045233-0.00719896603734-1.284040016250.682882996625-0.1421655739080.375538788882-0.176947445740.1596460434650.510563500264-0.128119074512-0.08037593765410.3948080592580.08361326723410.2456163779144.709187466123.29625364314-20.6684475875
293.86886297421-2.251208119522.367938435985.608096507584.002135595628.35508499320.07582611105450.3277152728310.451222200179-0.4062253146890.070293707187-0.0578890664884-0.4973764640090.134510380334-0.05597769419870.361846581822-0.0639165320948-0.03337711707910.245554036030.1139654026960.2816544828865.5322067751311.6596591166-17.0707915325
302.30211466866-3.41359363780.7479717323765.33814063087-2.494642762727.251948372840.182363924659-0.170910104383-1.594242260910.3779108962480.1105640865510.570287308540.732809803603-0.446107688466-0.1832974556940.319440652751-0.02306563045310.006263031866230.216687025894-0.03473339931790.353184079695-8.33176249943-20.76928089488.0691425567
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 56 )AA1 - 561 - 56
22chain 'A' and (resid 57 through 84 )AA57 - 8457 - 84
33chain 'A' and (resid 85 through 118 )AA85 - 11885 - 120
44chain 'A' and (resid 119 through 162 )AA119 - 162121 - 164
55chain 'A' and (resid 163 through 219 )AA163 - 219165 - 221
66chain 'A' and (resid 220 through 249 )AA220 - 249222 - 251
77chain 'A' and (resid 250 through 275 )AA250 - 275252 - 277
88chain 'B' and (resid 1 through 11 )BC1 - 111 - 11
99chain 'B' and (resid 12 through 19 )BC12 - 1912 - 19
1010chain 'B' and (resid 20 through 30 )BC20 - 3020 - 30
1111chain 'B' and (resid 31 through 41 )BC31 - 4131 - 41
1212chain 'B' and (resid 42 through 51 )BC42 - 5142 - 51
1313chain 'B' and (resid 52 through 71 )BC52 - 7152 - 71
1414chain 'B' and (resid 72 through 90 )BC72 - 9072 - 92
1515chain 'B' and (resid 91 through 99 )BC91 - 9993 - 101
1616chain 'C' and (resid 2 through 7 )CD2 - 72 - 7
1717chain 'D' and (resid 1 through 56 )DE1 - 561 - 56
1818chain 'D' and (resid 57 through 84 )DE57 - 8457 - 84
1919chain 'D' and (resid 85 through 137 )DE85 - 13785 - 139
2020chain 'D' and (resid 138 through 162 )DE138 - 162140 - 164
2121chain 'D' and (resid 163 through 249 )DE163 - 249165 - 251
2222chain 'D' and (resid 250 through 275 )DE250 - 275252 - 277
2323chain 'E' and (resid 1 through 11 )EF1 - 111 - 13
2424chain 'E' and (resid 12 through 30 )EF12 - 3014 - 32
2525chain 'E' and (resid 31 through 41 )EF31 - 4133 - 43
2626chain 'E' and (resid 42 through 51 )EF42 - 5144 - 53
2727chain 'E' and (resid 52 through 71 )EF52 - 7154 - 73
2828chain 'E' and (resid 72 through 90 )EF72 - 9074 - 92
2929chain 'E' and (resid 91 through 99 )EF91 - 9993 - 101
3030chain 'F' and (resid 2 through 7 )FG2 - 72 - 7

+
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