[English] 日本語
Yorodumi
- PDB-7re8: Class I MHC (HLA-A*02) presenting alpha fetoprotein peptide (AFP) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7re8
TitleClass I MHC (HLA-A*02) presenting alpha fetoprotein peptide (AFP)
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen, A-2 alpha chain
  • PHE-MET-ASN-LYS-PHE-ILE-TYR-GLU-ILE
KeywordsIMMUNE SYSTEM / Class I Major Histocompatibility Complex (HLA-A*02) / Alpha fetoprotein peptide (AFP).
Function / homology
Function and homology information


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 / Endosomal/Vacuolar pathway ...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 / 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 / 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 / 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 / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / 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
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 ...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 / MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsDasgupta, M. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Rep / Year: 2022
Title: Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma.
Authors: Liu, C. / Liu, H. / Dasgupta, M. / Hellman, L.M. / Zhang, X. / Qu, K. / Xue, H. / Wang, Y. / Fan, F. / Chang, Q. / Yu, D. / Ge, L. / Zhang, Y. / Cui, Z. / Zhang, P. / Heller, B. / Zhang, H. ...Authors: Liu, C. / Liu, H. / Dasgupta, M. / Hellman, L.M. / Zhang, X. / Qu, K. / Xue, H. / Wang, Y. / Fan, F. / Chang, Q. / Yu, D. / Ge, L. / Zhang, Y. / Cui, Z. / Zhang, P. / Heller, B. / Zhang, H. / Shi, B. / Baker, B.M. / Liu, C.
History
DepositionJul 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: PHE-MET-ASN-LYS-PHE-ILE-TYR-GLU-ILE
F: PHE-MET-ASN-LYS-PHE-ILE-TYR-GLU-ILE
D: MHC class I antigen, A-2 alpha chain
E: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,57924
Polymers90,1406
Non-polymers2,43918
Water1,04558
1
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: PHE-MET-ASN-LYS-PHE-ILE-TYR-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,29012
Polymers45,0703
Non-polymers1,2199
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-3 kcal/mol
Surface area18920 Å2
MethodPISA
2
F: PHE-MET-ASN-LYS-PHE-ILE-TYR-GLU-ILE
D: MHC class I antigen, A-2 alpha chain
E: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,29012
Polymers45,0703
Non-polymers1,2199
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint2 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.207, 87.310, 78.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 276 or resid 301 through 302 or resid 304 through 305))
21(chain D and (resid 2 through 276 or resid 301 through 302 or resid 304 through 305))
12(chain B and (resid 1 through 100 or resid 203))
22(chain E and (resid 1 through 100 or resid 201))
13chain C
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 276 or resid 301 through 302 or resid 304 through 305))A2 - 276
121(chain A and (resid 2 through 276 or resid 301 through 302 or resid 304 through 305))A301 - 302
131(chain A and (resid 2 through 276 or resid 301 through 302 or resid 304 through 305))A304 - 305
211(chain D and (resid 2 through 276 or resid 301 through 302 or resid 304 through 305))D2 - 276
221(chain D and (resid 2 through 276 or resid 301 through 302 or resid 304 through 305))D301 - 302
231(chain D and (resid 2 through 276 or resid 301 through 302 or resid 304 through 305))D304 - 305
112(chain B and (resid 1 through 100 or resid 203))B0
212(chain E and (resid 1 through 100 or resid 201))E0
113chain CC1 - 9
213chain FF1 - 9

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 2 types, 4 molecules ADBE

#1: Protein MHC class I antigen, A-2 alpha chain


Mass: 31985.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B8RNS7
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide PHE-MET-ASN-LYS-PHE-ILE-TYR-GLU-ILE


Mass: 1205.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 76 molecules

#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25 mM MES pH6.5, 150 mM NaCl, 25% v/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.82→58.48 Å / Num. obs: 20564 / % possible obs: 99 % / Redundancy: 6.5 % / CC1/2: 0.991 / Net I/σ(I): 8.4
Reflection shellResolution: 2.82→2.87 Å / Num. unique obs: 1016 / CC1/2: 0.918

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
PHENIXmodel building
DIALSdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5 / Resolution: 2.82→58.47 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 2019 10 %
Rwork0.1855 18163 -
obs0.191 20182 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.1 Å2 / Biso mean: 29.6049 Å2 / Biso min: 0.73 Å2
Refinement stepCycle: final / Resolution: 2.82→58.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6338 0 162 58 6558
Biso mean--40.86 21.08 -
Num. residues----768
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2703X-RAY DIFFRACTION9.627TORSIONAL
12D2703X-RAY DIFFRACTION9.627TORSIONAL
21B1007X-RAY DIFFRACTION9.627TORSIONAL
22E1007X-RAY DIFFRACTION9.627TORSIONAL
31C85X-RAY DIFFRACTION9.627TORSIONAL
32F85X-RAY DIFFRACTION9.627TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.82-2.890.27771410.23581234137594
2.89-2.970.27441370.2311252138994
2.97-3.060.31061410.23451254139596
3.06-3.150.28981450.2141280142595
3.15-3.270.28181420.2171277141996
3.27-3.40.29871410.21621275141698
3.4-3.550.28261350.20761258139395
3.55-3.740.21621530.18281340149399
3.74-3.970.24451430.17151312145599
3.98-4.280.20461460.15671308145499
4.28-4.710.19091500.142913231473100
4.71-5.390.1921500.143113451495100
5.4-6.790.21871460.18931333147998
6.79-58.470.21511490.18091372152199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.45570.7685-0.2832.314-0.94693.33840.0411-0.0223-0.026-0.124-0.1353-0.096-0.27920.209-0.30880.17480.05380.0120.1653-0.04350.04222.77793.140133.1089
23.87851.10781.07614.74310.31193.28850.0926-0.06060.28980.0786-0.12220.3685-0.2269-0.4021-0.14490.16250.00840.03430.2571-0.01730.148616.90221.754543.0975
31.8387-0.0286-1.36840.7898-1.01432.3375-0.0820.1915-0.02580.09940.0138-0.295-0.2604-0.2467-0.39770.2518-0.03190.00180.2155-0.0440.120931.49243.671538.1645
41.6903-0.34940.07910.4662-0.29671.61130.06130.08390.0341-0.2731-0.20620.06030.0491-0.00830.11370.24370.06430.01190.1489-0.04730.079728.9293-5.838426.2596
53.94420.8481-2.40092.8654-1.37794.2537-0.1574-0.1924-0.4194-0.2088-0.094-0.20620.1790.49450.15610.19280.01390.03940.1645-0.02520.197938.1742-9.529829.3966
62.31332.0847-1.0483.56310.64523.4850.0377-0.0277-0.3050.552-0.1905-0.1285-0.2115-0.2248-0.25520.26240.0417-0.03040.0616-0.00580.136619.5707-13.794444.1741
75.3188-1.2192.06152.7122-1.34113.17470.024-0.0821-0.2421-0.0010.33050.5266-0.4302-0.3564-0.31230.18630.0283-0.00090.1033-0.02390.2842-5.2672-6.153826.742
81.4203-0.14250.49671.48960.08292.27680.1310.2468-0.0576-0.44060.0963-0.058-0.06270.00773.06170.141-0.04310.01510.20420.03680.0151-3.6038-7.473120.0358
92.94680.07821.27341.5215-0.37542.16910.08260.3738-0.6015-0.32940.0826-0.06870.38580.1297-0.20480.16740.0172-0.05850.209-0.04020.2441-5.1179-8.924417.6447
101.1397-0.4011-0.94840.81290.14381.4231-0.2707-0.1098-0.32890.16810.02240.10640.33840.2156-0.69350.28560.1250.05390.21650.10030.13613.3446.559824.6345
114.3649-1.1416-1.12461.1227-0.16362.0384-0.01050.0550.66840.13670.0172-0.1844-0.47180.028-0.5570.19590.01940.03010.2639-0.05540.15339.23110.488828.0255
122.75090.72060.14921.4629-0.60071.63420.3346-0.00820.46740.0992-0.21450.2999-0.5088-0.23270.18670.26280.08470.00860.1998-0.01820.16491.648112.737824.422
131.94220.10480.02831.59560.45842.49140.1671-0.11580.11950.0872-0.17910.13430.3022-0.1167-0.19970.2003-0.0156-0.00130.1296-0.01280.02558.7237-46.146618.5223
141.24260.096-0.23992.50650.20884.32780.4170.0672-0.08940.4312-0.1939-0.30950.3150.33020.20630.1639-0.0316-0.06250.1960.0210.161514.6358-44.674428.4815
154.29372.36154.06382.38933.2225.6232-0.0020.22640.20910.2993-0.07140.30950.58810.2754-0.12150.10860.0220.04180.17050.03730.1710.0274-46.641423.6183
162.6746-0.26370.90180.1412-0.08451.8646-0.08990.10690.2029-0.2814-0.06240.2075-0.1714-0.05330.03020.24790.0515-0.02090.16390.03560.08892.6105-37.290411.5173
174.15580.83932.41892.22542.45343.5761-0.0324-0.26340.4671-0.2772-0.21020.0897-0.4016-0.2920.31860.24810.04970.00620.17520.04710.2351-6.6782-33.558814.8248
184.2387-0.332-1.08073.8576-2.10721.5312-0.2746-0.37360.150.5163-0.0001-0.181-0.1972-0.0418-0.53280.18750.0641-0.00960.0907-0.06980.211112.0355-29.120229.2593
196.6754-1.8937-4.22861.65881.89435.50970.3033-0.09410.2324-0.20580.0816-0.2273-0.24960.0424-0.34930.23530.0089-0.02640.06980.02590.22436.7393-36.842412.1435
202.3050.2961-1.17281.75-0.31022.94260.03090.14220.1581-0.21990.02420.0733-0.03670.1655-0.07870.14070.00590.00350.17240.01870.111235.3895-35.82383.0237
210.63360.25790.29872.1655-1.91022.14240.16560.31820.99010.43550.27040.0148-0.7468-0.01250.11310.3927-0.12050.14250.2997-0.0080.635840.2272-27.46128.0455
220.3536-0.12690.03081.40010.79962.87710.1257-0.04090.09760.0010.0653-0.1728-0.07340.02011.13970.3096-0.00910.01650.3547-0.16360.197611.5768-51.33351.13
232.3863-0.69460.53321.39640.10561.8118-0.0981-0.1605-0.30550.2368-0.0477-0.07590.1498-0.0367-0.15990.11350.0270.00910.09060.02030.085928.3968-51.998313.0264
241.2078-0.2477-1.03331.25671.01671.42120.0055-0.2205-0.33450.54740.22060.14780.3059-0.10942.52090.360.0206-0.09340.21940.16760.271727.9804-61.372618.4834
253.03710.04110.86960.8920.23620.3494-0.2437-0.07290.20030.2672-0.05760.01110.07260.0752-0.53220.20450.04290.03250.10670.04630.146919.8974-48.237214.3382
260.9813-0.6439-0.11640.5761-0.25660.73740.3510.5814-0.5659-0.2887-0.0644-0.35110.32850.32720.13970.30510.0917-0.01740.211-0.08840.45429.4052-59.61477.7114
275.49542.19480.56146.49151.66553.10840.16360.70740.4422-0.55320.1967-0.40720.15760.2509-0.30930.2770.05780.06610.18110.040.188335.1783-53.29536.5254
285.64563.971.69035.4104-1.43593.14060.7347-0.3441-0.27950.4106-0.3057-0.48190.13250.32740.50190.33190.0380.06710.18660.03010.194433.9977-3.832937.7657
295.23382.0161.61865.33470.51185.19680.2153-0.67790.77150.4692-0.08540.6288-0.6754-0.6620.9190.28790.11970.04430.2951-0.06310.3304-2.5289-39.18823.2734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 29 )A2 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 57 )A30 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 85 )A58 - 85
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 138 )A86 - 138
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 163 )A139 - 163
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 175 )A164 - 175
7X-RAY DIFFRACTION7chain 'A' and (resid 176 through 198 )A176 - 198
8X-RAY DIFFRACTION8chain 'A' and (resid 199 through 220 )A199 - 220
9X-RAY DIFFRACTION9chain 'A' and (resid 221 through 276 )A221 - 276
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 20 )B1 - 20
11X-RAY DIFFRACTION11chain 'B' and (resid 21 through 62 )B21 - 62
12X-RAY DIFFRACTION12chain 'B' and (resid 63 through 100 )B63 - 100
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 29 )D2 - 29
14X-RAY DIFFRACTION14chain 'D' and (resid 30 through 57 )D30 - 57
15X-RAY DIFFRACTION15chain 'D' and (resid 58 through 85 )D58 - 85
16X-RAY DIFFRACTION16chain 'D' and (resid 86 through 138 )D86 - 138
17X-RAY DIFFRACTION17chain 'D' and (resid 139 through 163 )D139 - 163
18X-RAY DIFFRACTION18chain 'D' and (resid 164 through 175 )D164 - 175
19X-RAY DIFFRACTION19chain 'D' and (resid 176 through 198 )D176 - 198
20X-RAY DIFFRACTION20chain 'D' and (resid 199 through 264 )D199 - 264
21X-RAY DIFFRACTION21chain 'D' and (resid 265 through 276 )D265 - 276
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 6 )E1 - 6
23X-RAY DIFFRACTION23chain 'E' and (resid 7 through 42 )E7 - 42
24X-RAY DIFFRACTION24chain 'E' and (resid 43 through 52 )E43 - 52
25X-RAY DIFFRACTION25chain 'E' and (resid 53 through 72 )E53 - 72
26X-RAY DIFFRACTION26chain 'E' and (resid 73 through 91 )E73 - 91
27X-RAY DIFFRACTION27chain 'E' and (resid 92 through 100 )E92 - 100
28X-RAY DIFFRACTION28chain 'C' and (resid 1 through 9 )C1 - 9
29X-RAY DIFFRACTION29chain 'F' and (resid 1 through 9 )F1 - 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