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- PDB-4nqv: Crystal Structure of HLA A*0101 in complex with NP44, an 9-mer in... -

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Basic information

Entry
Database: PDB / ID: 4nqv
TitleCrystal Structure of HLA A*0101 in complex with NP44, an 9-mer influenza epitope
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-1 alpha chain
  • Nucleoprotein
KeywordsImmune System/Viral Protein / immune system / HLA presenting H7N9 viral epitope / T cell receptor / Immune System-Viral Protein complex
Function / homology
Function and homology information


cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / vRNA Synthesis ...cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / vRNA Synthesis / Viral RNP Complexes in the Host Cell Nucleus / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Viral Messenger RNA Synthesis / positive regulation of CD8-positive, alpha-beta T cell proliferation / vRNP Assembly / helical viral capsid / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / Viral mRNA Translation / detection of bacterium / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / viral penetration into host nucleus / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / host cell / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Nucleoprotein / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
H7N9 subtype (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 Å
AuthorsRossjohn, J. / Gras, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Preexisting CD8+ T-cell immunity to the H7N9 influenza A virus varies across ethnicities.
Authors: Quinones-Parra, S. / Grant, E. / Loh, L. / Nguyen, T.H. / Campbell, K.A. / Tong, S.Y. / Miller, A. / Doherty, P.C. / Vijaykrishna, D. / Rossjohn, J. / Gras, S. / Kedzierska, K.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-1 alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, A-1 alpha chain
D: Beta-2-microglobulin
E: HLA class I histocompatibility antigen, A-1 alpha chain
F: Beta-2-microglobulin
G: HLA class I histocompatibility antigen, A-1 alpha chain
H: Beta-2-microglobulin
I: HLA class I histocompatibility antigen, A-1 alpha chain
J: Beta-2-microglobulin
K: HLA class I histocompatibility antigen, A-1 alpha chain
L: Beta-2-microglobulin
M: Nucleoprotein
N: Nucleoprotein
O: Nucleoprotein
P: Nucleoprotein
Q: Nucleoprotein
R: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)267,53118
Polymers267,53118
Non-polymers00
Water14,556808
1
A: HLA class I histocompatibility antigen, A-1 alpha chain
B: Beta-2-microglobulin
M: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)44,5893
Polymers44,5893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-17 kcal/mol
Surface area19250 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, A-1 alpha chain
D: Beta-2-microglobulin
N: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)44,5893
Polymers44,5893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-15 kcal/mol
Surface area19060 Å2
MethodPISA
3
E: HLA class I histocompatibility antigen, A-1 alpha chain
F: Beta-2-microglobulin
O: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)44,5893
Polymers44,5893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-13 kcal/mol
Surface area19300 Å2
MethodPISA
4
G: HLA class I histocompatibility antigen, A-1 alpha chain
H: Beta-2-microglobulin
P: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)44,5893
Polymers44,5893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-17 kcal/mol
Surface area19410 Å2
MethodPISA
5
I: HLA class I histocompatibility antigen, A-1 alpha chain
J: Beta-2-microglobulin
Q: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)44,5893
Polymers44,5893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-17 kcal/mol
Surface area19620 Å2
MethodPISA
6
K: HLA class I histocompatibility antigen, A-1 alpha chain
L: Beta-2-microglobulin
R: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)44,5893
Polymers44,5893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-20 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.538, 81.496, 140.071
Angle α, β, γ (deg.)90.000, 121.580, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
HLA class I histocompatibility antigen, A-1 alpha chain / MHC class I antigen A*1


Mass: 31636.955 Da / Num. of mol.: 6 / Fragment: UNP residues 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P30443, UniProt: P04439*PLUS
#2: Protein
Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 6 / 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
#3: Protein/peptide
Nucleoprotein


Mass: 1072.210 Da / Num. of mol.: 6 / Fragment: NP44, 9-mer influenza epitope / Source method: obtained synthetically / Source: (synth.) H7N9 subtype (virus) / References: UniProt: P03466*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE 9-MER PEPTIDE NP44 IS INFLUENZA EPITOPE. BUT THE EPITOPE IS SHARED BY MANY STRAINS, THUS IT IS ...THE 9-MER PEPTIDE NP44 IS INFLUENZA EPITOPE. BUT THE EPITOPE IS SHARED BY MANY STRAINS, THUS IT IS NOT APPROPRIATE TO ASSIGN A UNP REFERENCE OF SPECIFIC STRAIN.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.6
Details: 0.2M MgCl, 0.1M Na-citrate pH 5.6, 15-20% PEG 6K, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.39→43.492 Å / Num. all: 100231 / Num. obs: 100231 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 61 Å2 / Rsym value: 0.105 / Net I/σ(I): 10.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BO8

3bo8


Resolution: 2.39→43.49 Å / Cor.coef. Fo:Fc: 0.9071 / Cor.coef. Fo:Fc free: 0.87 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.585 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2914 4976 4.98 %RANDOM
Rwork0.2555 ---
all0.25 ---
obs0.2573 99957 98.78 %-
Displacement parametersBiso max: 175.7 Å2 / Biso mean: 62.5528 Å2 / Biso min: 15.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.2443 Å20 Å2-1.121 Å2
2--2.4323 Å20 Å2
3----2.1881 Å2
Refine analyzeLuzzati coordinate error obs: 0.553 Å
Refinement stepCycle: LAST / Resolution: 2.39→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18820 0 0 808 19628
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8863SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes546HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2801HARMONIC5
X-RAY DIFFRACTIONt_it19318HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2387SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact21268SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d19318HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg26174HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion3.51
LS refinement shellResolution: 2.39→2.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3059 321 4.73 %
Rwork0.2742 6466 -
all0.2757 6787 -
obs--98.78 %
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)
11.7184-0.6820.4234.52590.22865.0469-0.1094-0.0885-0.1302-0.04080.19130.07210.3731-0.1397-0.08190.0546-0.00730.01770.01290.06080.070323.263-5.127461.5385
21.09151.1473-0.29953.3637-0.77540.7894-0.15410.0404-0.1024-0.8380.2812-0.2365-0.01220.2767-0.12710.6006-0.19450.07420.269-0.07310.021933.693415.418935.3807
32.7859-0.1659-0.05463.2460.9767-0.182-0.52790.06330.2331-0.3879-0.39980.3211-0.11140.02950.92770.3966-0.0118-0.17490.16920.06540.210617.355614.419641.9465
41.3029-0.8173-0.05422.6057-0.65482.8612-0.10580.09610.3343-0.47990.21260.6246-0.2076-0.326-0.10680.22390.0004-0.13160.22960.10150.331813.154515.214746.3968
53.362-2.24420.55274.6335-1.16981.4779-0.09480.08440.3091-0.1618-0.0797-0.5529-0.28530.10640.17450.5832-0.0776-0.00410.1369-0.00180.16929.4558.9532-0.496
60.89840.49930.39235.50390.96450.3847-0.17620.1873-0.22680.024-0.0609-0.0570.2372-0.03790.23710.4145-0.00270.09360.176-0.1050.294729.2669-26.55646.7627
79.1352-4.69372.33791.7681-0.680510.0664-0.0976-0.1620.51410.24690.12940.3776-0.5158-0.4222-0.03190.4890.08420.02870.36590.04220.385817.87260.823917.1246
82.8158-1.29471.59842.29-1.34443.7642-0.188-0.4119-0.08490.20210.0631-0.283-0.31380.16760.12490.46020.0213-0.06110.2661-0.01870.129336.4695-8.937819.2271
92.46311.1234-0.12715.0724-0.33531.99580.0468-0.0460.12410.0611-0.16930.414-0.13350.00050.12250.2630.05760.0150.0852-0.04610.522568.2669.178563.3602
100.93690.4538-0.04334.80540.44370.423-0.2366-0.1255-0.2453-0.2072-0.0698-0.0020.2835-0.07570.30650.34450.01290.05360.16760.05940.577569.0214-26.07855.3413
110.5867-2.96150.99072.829-0.12854.39620.0119-0.2336-0.1805-0.3608-0.15290.10680.0714-0.28660.1410.33580.0186-0.20350.2109-0.01410.388262.606-8.965446.7868
12-0.4406-0.3399-0.450.57170.49872.63440.08110.14470.039-0.3611-0.09920.21210.1138-0.23520.01810.65830.0201-0.27870.33770.0040.557360.5247-7.628341.8324
134.34031.0539-1.84051.82220.67583.47970.0793-0.5555-0.14970.19-0.0190.3609-0.32420.287-0.06030.67270.10760.29360.14820.10170.360492.38-17.492239.9079
141.8560.97230.02873.5654-0.4951.18780.1931-0.08040.1576-0.255-0.1138-0.1592-0.30060.0351-0.07930.3981-0.02580.05350.11520.0820.2604111.9547-5.605912.1269
153.2918-2.25610.17530.07160.66050.5758-0.2852-0.0294-0.12780.21890.3415-0.4107-0.04310.3629-0.05640.4618-0.0353-0.12040.33510.0460.2055116.7874-20.36629.1369
164.6409-0.473-1.24441.15191.0399-0.02060.0541-0.2258-0.26150.2390.0296-0.21530.04360.544-0.08360.47230.0731-0.03110.34340.13570.1767116.513-20.723728.1626
172.3471-0.233-0.78696.59562.54685.5434-0.2994-0.0513-0.12750.53860.4153-0.14790.54610.4229-0.11590.13220.07880.0610.1297-0.01220.164972.3147-5.5968-0.6609
181.1169-0.1321-0.65030.85560.93682.5049-0.1644-0.159-0.08880.71990.2040.17720.40020.0093-0.03960.78470.07220.15690.24910.04070.102760.63717.71824.3782
191.7448-0.4978-0.14334.97050.05751.79-0.15940.0197-0.14050.40790.2157-0.41050.22040.1655-0.05630.415-0.1309-0.13670.27820.02630.289975.766315.086613.7271
201.36421.9531.35972.29762.09453.1446-0.1204-0.14650.28420.7610.2725-0.82680.03120.4321-0.15210.33660.0184-0.16480.368-0.1660.482782.379214.783115.0778
211.8154-0.3131-0.4750.7340.03524.3186-0.1138-0.6322-0.02970.78970.0917-0.19970.05310.04260.02211.2776-0.22780.08850.5073-0.01970.175360.163124.1997104.309
222.7318-0.2669-2.09113.48550.07152.2054-0.0826-0.1944-0.04690.3411-0.089-0.2352-0.09390.10660.17160.29960.01930.00120.14920.06080.261261.483228.570884.5307
233.3672-0.6474-0.4560.83041.01972.0274-0.017-0.4642-0.00930.4669-0.0464-0.85080.15910.5360.06350.4225-0.0658-0.26190.38270.13130.51576.953121.464688.9019
240.4292-1.00051.21940.35211.52011.34850.0206-0.1733-0.39970.58670.0458-0.4995-0.22090.6238-0.06650.6484-0.1317-0.22010.41930.23470.675380.630319.575390.0387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|172 }A1 - 172
2X-RAY DIFFRACTION2{ A|173 - A|274 }A173 - 274
3X-RAY DIFFRACTION3{ B|0 - B|23 }B0 - 23
4X-RAY DIFFRACTION4{ B|24 - B|99 }B24 - 99
5X-RAY DIFFRACTION5{ C|1 - C|183 }C1 - 183
6X-RAY DIFFRACTION6{ C|184 - C|274 }C184 - 274
7X-RAY DIFFRACTION7{ D|0 - D|4 }D0 - 4
8X-RAY DIFFRACTION8{ D|5 - D|99 }D5 - 99
9X-RAY DIFFRACTION9{ E|1 - E|183 }E1 - 183
10X-RAY DIFFRACTION10{ E|184 - E|274 }E184 - 274
11X-RAY DIFFRACTION11{ F|1 - F|35 }F1 - 35
12X-RAY DIFFRACTION12{ F|36 - F|99 }F36 - 99
13X-RAY DIFFRACTION13{ G|1 - G|181 }G1 - 181
14X-RAY DIFFRACTION14{ G|182 - G|274 }G182 - 274
15X-RAY DIFFRACTION15{ H|0 - H|48 }H0 - 48
16X-RAY DIFFRACTION16{ H|49 - H|99 }H49 - 99
17X-RAY DIFFRACTION17{ I|1 - I|181 }I1 - 181
18X-RAY DIFFRACTION18{ I|182 - I|274 }I182 - 274
19X-RAY DIFFRACTION19{ J|0 - J|16 }J0 - 16
20X-RAY DIFFRACTION20{ J|17 - J|99 }J17 - 99
21X-RAY DIFFRACTION21{ K|1 - K|77 }K1 - 77
22X-RAY DIFFRACTION22{ K|78 - K|274 }K78 - 274
23X-RAY DIFFRACTION23{ L|0 - L|39 }L0 - 39
24X-RAY DIFFRACTION24{ L|40 - L|99 }L40 - 99

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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

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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

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