[English] 日本語
Yorodumi
- PDB-7k80: KIR3DL1*001 in complex with HLA-A*24:02 presenting the RYPLTFGW p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k80
TitleKIR3DL1*001 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide
Components
  • ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP
  • Beta-2-microglobulin
  • Killer cell immunoglobulin-like receptor 3DL1
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / KIR receptor / HLA / peptide presentation
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / HLA-B specific inhibitory MHC class I receptor activity / Late Phase of HIV Life Cycle / Nef Mediated CD8 Down-regulation / immune response-regulating signaling pathway / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host autophagy / Nef Mediated CD4 Down-regulation / Nef and signal transduction ...Nef mediated downregulation of CD28 cell surface expression / HLA-B specific inhibitory MHC class I receptor activity / Late Phase of HIV Life Cycle / Nef Mediated CD8 Down-regulation / immune response-regulating signaling pathway / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host autophagy / Nef Mediated CD4 Down-regulation / Nef and signal transduction / natural killer cell mediated cytotoxicity / Uncoating of the HIV Virion / antigen processing and presentation of peptide antigen via MHC class I / host cell Golgi membrane / Binding and entry of HIV virion / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / Assembly Of The HIV Virion / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / Budding and maturation of HIV virion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / SH3 domain binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / virion component / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / molecular adaptor activity / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
HIV-1 Nef protein, anchor domain superfamily / : / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains ...HIV-1 Nef protein, anchor domain superfamily / : / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Immunoglobulin / Immunoglobulin domain / 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 subtype / Immunoglobulin / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / MHC class I antigen / MHC class I antigen / Protein Nef / Killer cell immunoglobulin-like receptor 3DL1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMacLachlan, B.J. / Rossjohn, J. / Vivian, J.P.
CitationJournal: J Immunol. / Year: 2021
Title: The Role of the HLA Class I alpha 2 Helix in Determining Ligand Hierarchy for the Killer Cell Ig-like Receptor 3DL1.
Authors: Saunders, P.M. / MacLachlan, B.J. / Widjaja, J. / Wong, S.C. / Oates, C.V.L. / Rossjohn, J. / Vivian, J.P. / Brooks, A.G.
History
DepositionSep 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP
D: MHC class I antigen
E: Beta-2-microglobulin
F: ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP
G: Killer cell immunoglobulin-like receptor 3DL1
H: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,99619
Polymers155,5488
Non-polymers1,44711
Water3,513195
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5439
Polymers77,7744
Non-polymers7695
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP
H: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,45310
Polymers77,7744
Non-polymers6796
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.265, 85.017, 94.832
Angle α, β, γ (deg.)82.47, 85.97, 77.92
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 3 types, 6 molecules ADBEGH

#1: Protein MHC class I antigen


Mass: 31778.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET-30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A411J078, UniProt: A0A5H2UYS3*PLUS
#2: Protein 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 / Plasmid: pET-30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61769
#4: Protein Killer cell immunoglobulin-like receptor 3DL1 / CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / MHC class I NK ...CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / MHC class I NK cell receptor / Natural killer-associated transcript 3 / NKAT-3 / p70 natural killer cell receptor clones CL-2/CL-11 / p70 NK receptor CL-2/CL-11


Mass: 33076.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1, CD158E, NKAT3, NKB1 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P43629

-
Protein/peptide / Sugars , 2 types, 7 molecules CF

#3: Protein/peptide ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP


Mass: 1040.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P04601*PLUS
#7: 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.: 5 / 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 , 3 types, 201 molecules

#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14% PEG 3350, 2% tacsimate, pH 5.0, and 0.1 M trisodium citrate, pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.4→43.09 Å / Num. obs: 58740 / % possible obs: 97 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.47 / Num. unique obs: 3718 / % possible all: 91

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VH8

3vh8


Resolution: 2.4→40 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 2980 5.07 %
Rwork0.198 --
obs0.2006 58740 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10708 0 93 195 10996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411124
X-RAY DIFFRACTIONf_angle_d0.75915095
X-RAY DIFFRACTIONf_dihedral_angle_d15.2071515
X-RAY DIFFRACTIONf_chiral_restr0.0551561
X-RAY DIFFRACTIONf_plane_restr0.0041975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.36841360.31432377X-RAY DIFFRACTION85
2.44-2.480.3741270.29272641X-RAY DIFFRACTION97
2.48-2.530.32491390.29382674X-RAY DIFFRACTION97
2.53-2.580.34811480.28372719X-RAY DIFFRACTION98
2.58-2.630.30511420.27912600X-RAY DIFFRACTION98
2.63-2.690.36451370.27982693X-RAY DIFFRACTION98
2.69-2.750.30071360.25652664X-RAY DIFFRACTION98
2.75-2.820.33631390.25012714X-RAY DIFFRACTION98
2.82-2.890.29391380.24892674X-RAY DIFFRACTION98
2.89-2.980.30911550.24532687X-RAY DIFFRACTION98
2.98-3.070.30011400.23812668X-RAY DIFFRACTION98
3.07-3.180.27271610.22862692X-RAY DIFFRACTION98
3.18-3.310.29351300.20892662X-RAY DIFFRACTION98
3.31-3.460.2371300.19772713X-RAY DIFFRACTION98
3.46-3.640.21341520.17942667X-RAY DIFFRACTION98
3.65-3.870.23361390.17552694X-RAY DIFFRACTION98
3.87-4.170.2181270.16282659X-RAY DIFFRACTION97
4.17-4.590.19681540.15112672X-RAY DIFFRACTION97
4.59-5.250.20181570.15042622X-RAY DIFFRACTION96
5.25-6.620.24481510.18152656X-RAY DIFFRACTION97
6.62-43.090.21251420.1722612X-RAY DIFFRACTION95
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)
13.1199-1.85881.14578.7992-3.02426.44010.02150.0356-0.0476-0.0369-0.3797-0.66620.83650.15730.36680.4927-0.05470.08010.301-0.01770.39155.0756-3.9164-10.3169
22.9476-1.15613.952.4923-3.33517.35210.68550.5033-0.676-1.0916-0.64530.40881.3713-0.05830.12440.7156-0.15070.12370.5333-0.0590.5259-1.2452-4.0502-20.7917
33.70781.32990.1157.2494-1.10613.09160.025-0.4169-0.26240.6522-0.14370.3320.6905-0.95220.01920.6155-0.2340.11510.7509-0.11160.387-12.1742-4.4127-10.2171
47.0843-1.75365.88741.8821-3.58437.9156-0.13770.0155-1.0295-0.07380.3950.18931.1144-0.8978-0.16230.9495-0.32370.1370.6723-0.0790.491-10.1552-13.6196-13.6783
53.42650.19180.51115.79791.22215.4485-0.3866-0.79150.13120.3846-0.08030.2461-0.5342-0.46380.28650.89390.1105-0.03740.63780.03530.50132.20260.515319.6545
66.0935-1.0284-0.39966.05130.98996.6092-0.5882-0.9279-0.00821.15430.17830.3940.1465-1.4410.18210.9280.1398-0.01590.7244-0.06420.4862-1.70321.665222.9957
78.3052-3.47154.7267.8723-4.38715.86630.4299-0.21960.1928-0.0945-0.37850.2390.5333-0.59680.02750.61540.03810.03110.3245-0.15450.2614-1.432311.98322.2878
86.67942.15552.03930.7460.82081.10960.2198-0.3464-0.59771.9988-0.6169-2.27070.40311.0667-0.08481.09190.0269-0.49720.55650.12660.930618.70265.272615.2996
92.60161.40682.3856.39992.2094.5167-0.1201-0.3462-0.18150.2976-0.0669-0.4859-0.0224-0.1560.2720.4553-0.0262-0.00890.3699-0.03570.35247.474911.12580.9157
106.09934.42132.69158.44014.54545.7153-0.3583-0.1473-0.48660.12810.1444-0.76950.0695-0.12820.29030.48990.0436-0.08020.33530.08220.33837.30918.2912-2.1909
117.16433.54584.78015.68513.21497.9292-0.3988-0.36510.460.68740.0578-0.5321-0.43570.50280.14250.5548-0.0357-0.12450.4053-0.0820.48114.168310.63636.2155
127.66747.5234.53457.62245.02953.9472-0.33820.08790.05440.27840.15920.4484-0.7456-0.17470.36650.50770.0591-0.05360.4491-0.03330.43544.492419.88530.0785
134.5059-0.1772-2.85739.53490.96983.44880.0571-1.5509-0.32252.45510.793-0.38130.30.7812-0.2521.20010.1544-0.31390.5198-0.19460.42599.187815.695413.2939
148.1817-3.18533.46844.94481.79714.1024-0.1329-0.7933-2.63280.69630.56621.081.3492-0.9078-0.14520.8027-0.26330.05310.77210.20160.6721-5.8579-8.5775-17.7383
153.9735-1.38541.074.9271-1.52634.9973-0.04870.18560.19050.0951-0.2904-0.8289-0.22020.60550.29630.22540.05220.00770.32980.00790.439343.411143.407236.792
163.1151-1.42863.40632.5212-2.96685.1980.14060.2097-0.1374-0.625-0.0927-0.10860.16570.4362-0.17690.29020.08370.03350.3841-0.02430.458837.008242.864626.1849
173.7001-1.20172.11193.2849-4.00178.38950.1276-0.0949-0.18280.05840.01950.47540.0579-0.3394-0.20950.14920.0630.05690.3319-0.04490.444929.059242.640237.0168
182.30151.35840.73362.97470.25414.0750.14730.1127-0.1640.038-0.14840.27320.2004-0.3648-0.00330.19360.00680.05740.3168-0.02810.384625.986135.650834.3791
194.0219-1.4955-2.48276.51476.82768.53070.0903-0.6670.34620.5534-0.23040.0692-0.04670.08180.03720.6569-0.0389-0.0270.47520.0010.388139.858447.907366.6639
204.8608-1.281-2.46945.03774.0667.7956-0.0693-0.64850.26081.2147-0.18820.60340.6317-0.47970.43660.7118-0.09360.0660.5518-0.06730.466935.972248.849469.8471
213.8924-1.40393.92689.5319-3.34954.36480.59930.30050.1669-0.4023-0.25881.91110.8377-0.4155-0.21910.44040.0746-0.01560.4924-0.09740.784928.902760.330942.6986
228.66881.68810.1485.94961.42095.02150.2274-0.3994-0.41121.5618-0.268-0.97220.26320.8242-0.29210.5983-0.0958-0.23840.40810.07220.513749.98155.575859.3836
235.88430.52375.53046.88690.99215.12260.2755-0.91170.27960.8012-0.3242-0.9531-0.1101-0.1460.2620.4545-0.1038-0.06590.4099-0.00890.443145.968355.638751.8878
247.36673.02217.44937.09256.7269.9804-1.01521.04760.7412-0.66670.36610.3928-1.010.75870.53420.5429-0.0084-0.01540.3056-0.00170.40943.096662.239643.9656
254.02013.9944.23973.51994.54194.8732-0.37780.23590.0602-0.18670.3927-0.3395-0.33840.4528-0.110.40650.0285-0.05280.40460.02610.473944.280855.834344.7015
266.36825.80036.88535.03725.71127.67710.36250.0866-0.28020.6617-0.0331-0.7903-0.03630.7021-0.47740.5671-0.092-0.10120.4742-0.02010.618951.331159.064353.3303
279.4138-0.29833.67757.93913.56685.3994-0.0118-0.40.32190.5702-0.01730.0936-0.50340.0046-0.02270.5449-0.0801-0.00710.2751-0.01840.424942.948865.702952.9049
288.7445-0.86286.32277.8408-2.64616.491-0.10950.5948-1.54540.23320.3960.99450.03160.3077-0.38180.29620.0710.14450.47320.15650.554732.678538.268229.4335
295.23212.92172.57474.03653.42518.24120.1745-0.60640.30150.1947-0.2617-0.0333-0.84840.25770.1750.444-0.04810.03730.42350.06120.40488.906321.7876-31.7912
306.45214.5726-1.63725.2986-1.42511.92090.1023-0.0635-0.48390.0248-0.3368-0.54740.08620.18470.28630.27630.0784-0.00130.3537-0.04040.3733-2.13871.0246-43.8219
317.48782.88672.11686.95440.612.02010.0149-0.15620.4379-0.6741-0.1620.6661-0.2332-0.08690.17310.3680.00370.00090.432-0.11140.501-27.172-7.7733-40.8936
323.77591.28960.17634.35263.01876.6724-0.0564-0.19770.3224-0.59350.3019-0.3899-1.60811.1056-0.17230.9064-0.25250.11430.70950.09670.603446.164168.774814.9155
336.3113.7138-1.09514.6947-1.79993.7963-0.08210.1085-0.0792-0.5483-0.2225-0.3556-0.35610.74120.33960.5510.02350.0460.4122-0.04530.387333.37647.06323.1417
347.7297-0.14383.25737.10252.59155.7251-0.14880.1657-0.0266-0.7698-0.08730.6032-0.4468-0.55310.19110.37280.0703-0.08340.3606-0.01820.43112.444638.12499.782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 174 )
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 11 )
8X-RAY DIFFRACTION8chain 'B' and (resid 12 through 19 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 41 )
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 61 )
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 99 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 8 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 56 )
16X-RAY DIFFRACTION16chain 'D' and (resid 57 through 84 )
17X-RAY DIFFRACTION17chain 'D' and (resid 85 through 118 )
18X-RAY DIFFRACTION18chain 'D' and (resid 119 through 174 )
19X-RAY DIFFRACTION19chain 'D' and (resid 175 through 219 )
20X-RAY DIFFRACTION20chain 'D' and (resid 220 through 276 )
21X-RAY DIFFRACTION21chain 'E' and (resid 0 through 5 )
22X-RAY DIFFRACTION22chain 'E' and (resid 6 through 19 )
23X-RAY DIFFRACTION23chain 'E' and (resid 20 through 30 )
24X-RAY DIFFRACTION24chain 'E' and (resid 31 through 41 )
25X-RAY DIFFRACTION25chain 'E' and (resid 42 through 61 )
26X-RAY DIFFRACTION26chain 'E' and (resid 62 through 77 )
27X-RAY DIFFRACTION27chain 'E' and (resid 78 through 99 )
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 8 )
29X-RAY DIFFRACTION29chain 'G' and (resid 6 through 108 )
30X-RAY DIFFRACTION30chain 'G' and (resid 109 through 208 )
31X-RAY DIFFRACTION31chain 'G' and (resid 209 through 295 )
32X-RAY DIFFRACTION32chain 'H' and (resid 6 through 108 )
33X-RAY DIFFRACTION33chain 'H' and (resid 109 through 225 )
34X-RAY DIFFRACTION34chain 'H' and (resid 226 through 294 )

+
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