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- PDB-7p0a: CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY ... -

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Basic information

Entry
Database: PDB / ID: 7p0a
TitleCRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 PEPTIDE with D-AMINOACID (p3P6f)
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Stable signal peptide
KeywordsIMMUNE SYSTEM / D-aminoacid / class I major histocompatibility complex / b2-microglobulin
Function / homology
Function and homology information


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 / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / receptor-mediated endocytosis of virus by host cell ...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 / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / receptor-mediated endocytosis of virus by host cell / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / 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 / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / host cell endoplasmic reticulum membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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 ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.429 Å
AuthorsBroggini, L. / Ricagno, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Omega / Year: 2022
Title: l- to d-Amino Acid Substitution in the Immunodominant LCMV-Derived Epitope gp33 Highlights the Sensitivity of the TCR Recognition Mechanism for the MHC/Peptide Structure and Dynamics.
Authors: Ballabio, F. / Broggini, L. / Paissoni, C. / Han, X. / Peqini, K. / Sala, B.M. / Sun, R. / Sandalova, T. / Barbiroli, A. / Achour, A. / Pellegrino, S. / Ricagno, S. / Camilloni, C.
History
DepositionJun 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Stable signal peptide
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Stable signal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,69414
Polymers90,0476
Non-polymers6478
Water2,126118
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Stable signal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3126
Polymers45,0243
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-55 kcal/mol
Surface area17940 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Stable signal peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3838
Polymers45,0243
Non-polymers3595
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-50 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.649, 125.958, 92.927
Angle α, β, γ (deg.)90.00, 126.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32087.703 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11892.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Stable signal peptide / SSP


Mass: 1043.215 Da / Num. of mol.: 2 / Mutation: Phe6DPN / Source method: obtained synthetically / Details: Derived peptide gp33-41 from LCMV
Source: (synth.) Lymphocytic choriomeningitis virus (strain Armstrong)
References: UniProt: P09991

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Non-polymers , 3 types, 126 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.7 M Ammonium Sulphate, 100 mM Tris-HCl, pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.429→48.409 Å / Num. obs: 30282 / % possible obs: 93.2 % / Redundancy: 6.5 % / CC1/2: 0.994 / Net I/σ(I): 2
Reflection shellResolution: 2.43→2.68 Å / Num. unique obs: 30282 / CC1/2: 0.591

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
STARANISOdata scaling
Cootmodel building
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NSK

4nsk


Resolution: 2.429→48.409 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1989 6.57 %
Rwork0.2103 --
obs0.2134 30282 72.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.429→48.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5573 0 32 118 5723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035771
X-RAY DIFFRACTIONf_angle_d0.6787886
X-RAY DIFFRACTIONf_dihedral_angle_d3.3463323
X-RAY DIFFRACTIONf_chiral_restr0.044821
X-RAY DIFFRACTIONf_plane_restr0.0041017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.480.469260.307763X-RAY DIFFRACTION2
2.4896-2.55690.5836160.355307X-RAY DIFFRACTION11
2.5569-2.63210.341570.3416662X-RAY DIFFRACTION24
2.6321-2.71710.3941880.36071179X-RAY DIFFRACTION42
2.7171-2.81420.42051100.32461736X-RAY DIFFRACTION62
2.8142-2.92680.37351410.30772106X-RAY DIFFRACTION76
2.9268-3.060.38051860.28832605X-RAY DIFFRACTION93
3.06-3.22130.30432040.26942780X-RAY DIFFRACTION100
3.2213-3.42310.26751920.23712806X-RAY DIFFRACTION100
3.4231-3.68730.24042090.21552793X-RAY DIFFRACTION100
3.6873-4.05820.2431990.18772799X-RAY DIFFRACTION100
4.0582-4.6450.22111970.16032819X-RAY DIFFRACTION100
4.645-5.85060.21181880.17912803X-RAY DIFFRACTION99
5.8506-48.40.25361960.2082835X-RAY DIFFRACTION99
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)
15.35661.0196-1.00341.71480.23993.0292-0.0441-0.6086-0.54350.7075-0.33850.2150.3826-0.84210.27040.3305-0.09510.15740.46930.06450.2637-20.5657-5.697812.2572
24.3956-0.90470.22844.91411.14283.224-0.07220.1380.5773-0.39480.01210.4161-0.7313-0.4332-0.0270.37410.09880.04880.1550.08950.2949-15.66517.7762.887
33.6933-0.81813.92693.95110.54868.2278-0.6012-0.80191.17671.2743-0.1689-0.4491-1.2021-0.27020.68161.21980.02340.07040.6344-0.07830.6905-9.468710.685134.6434
48.5933-1.7422-6.75023.51421.66155.381-0.2508-0.57680.1980.09620.1331-0.53530.61772.01820.15330.27470.0779-0.00770.62420.15150.4972-1.5659-5.250625.9314
56.64872.04716.34372.9063.91527.75170.0244-0.2952-0.38952.5781.4780.1819-1.31980.4466-1.22451.41890.26950.39221.32650.08940.5601-10.8452-2.85648.0963
62.81860.99580.83813.4522-3.83315.7632-0.1579-0.4074-0.02950.930.11070.0014-0.82470.5199-0.06050.74860.0117-0.04230.52170.15060.2526-9.504-5.692935.1316
72.5253-1.26891.79253.656-3.20523.07790.18-0.4757-0.51011.02350.0222-0.0640.21190.0162-0.24040.57060.089-0.00160.65920.15730.2892-5.625-11.789124.1456
87.6195-7.97786.57728.3479-6.96.4725-0.8045-1.4873-1.54540.17341.19720.44840.93040.1146-0.18581.15940.05110.30011.27870.35550.7504-10.3422-17.330236.1221
91.59691.4767-1.52491.412-1.91916.4773-0.4556-1.2225-0.41430.72990.57890.075-0.0638-0.9095-0.18550.51160.3663-0.03011.11390.1440.4953-14.1408-5.360520.8614
100.193-0.8581.04563.7911-4.55126.2275-0.1688-0.4642-0.04490.7381-0.2905-0.4095-0.9890.26060.41970.71290.2879-0.12580.27710.2923-0.0233-8.1735-0.509317.2703
110.28610.0432-0.68231.14470.191.68820.3525-2.0931-0.06250.9457-0.1363-0.32730.42340.56560.1650.9270.15620.15411.49790.21250.5391-9.2305-10.53541.2443
127.92210.9954-2.63266.72331.81891.5758-1.0161-0.6592-0.348-0.1980.4555-0.2419-0.1273-0.18070.18940.57770.21890.10960.63540.16170.3403-3.1108-14.467533.0282
131.9151-3.61363.31269.4245-9.08769.3439-0.0943-0.0284-1.3006-0.03220.2773-0.41911.0071.2331-0.04830.63540.30490.12481.04760.30260.64962.2542-14.877221.3515
144.0832-0.3896-4.69055.6815-4.17919.1861-0.0363-2.08961.14961.10060.336-1.5122-0.57381.7139-0.25330.76990.0939-0.24231.4695-0.01730.62660.3946-7.425239.0539
155.4595-2.53350.0593.42722.95393.9486-1.20130.0251-1.1152-0.4381-0.38970.96090.2245-0.77451.35450.34830.05510.04020.53080.02270.5531-22.9061-0.83612.6452
165.5196-0.8271-2.05243.30111.13244.74130.3815-0.98920.69890.95460.1051-0.274-0.5380.0017-0.50260.7041-0.0188-0.17680.6879-0.13460.5169-7.871747.815722.4119
173.7437-0.138-0.86766.1667-0.93542.1059-0.0704-0.9785-0.27110.6245-0.06820.17030.29440.40740.08750.72560.1296-0.08360.41480.03950.4684-12.289634.012617.5433
185.66311.8910.84445.05521.88675.4583-0.66140.3186-0.5704-0.79790.4022.14790.91550.08440.21660.88160.0302-0.14660.43720.05321.3951-36.223829.145611.3698
195.1819-1.5915-6.72531.62791.83118.7577-0.20940.4031-2.3096-0.0682-0.5769-0.0866-0.6212-0.29960.6030.40860.1073-0.02760.40110.09710.5554-25.360646.88736.5977
200.37190.3142-0.11940.2673-0.10010.0374-0.37070.0938-1.26420.2541-0.00250.12360.41680.51030.45060.5380.44860.39021.40260.43641.5346-44.093845.748819.9573
217.5849-0.05480.66988.1494-1.89750.4938-0.5357-1.34890.20551.72330.78240.873-0.7586-0.7916-0.31730.39660.1623-0.0420.60930.30050.4371-32.950347.994916.1148
224.0919-2.5609-3.71693.37560.87014.56870.1586-0.4457-0.46330.3028-0.54060.2015-0.70220.35710.26650.5330.0835-0.27190.4818-0.10210.7656-17.107150.86858.4688
236.7952-6.6619-6.46167.23855.04838.46830.0163-0.6580.9281-0.06380.0577-0.5394-1.03780.1692-0.13520.64190.0804-0.41620.5314-0.16990.3392-31.274758.347712.0459
245.0647-5.75475.62657.5331-6.04336.9518-0.8095-1.4440.86971.61530.8296-0.3236-0.7343-0.0588-0.03720.80890.2091-0.06260.8495-0.26630.4696-33.960959.917616.3757
252.64921.1569-1.61433.42271.47952.6188-0.5085-2.4940.00091.52490.9775-0.1498-0.2006-0.4806-0.43210.70560.0891-0.19631.1672-0.06030.4921-17.975647.265517.6692
265.438-0.3889-4.09011.78341.24713.5951-0.1554-0.8971-0.80190.84640.1773-0.0724-0.0914-0.9636-0.32760.23010.189-0.30920.89490.39080.3831-24.488746.883515.1679
271.58921.39650.93832.24881.08530.62130.1192-2.18550.25440.46170.07611.8392-0.1175-0.7163-0.49460.49810.01630.10011.03070.23560.7208-47.279154.729712.5957
284.66970.2765-6.11375.83620.33298.20950.732-0.95420.25810.3903-0.2687-0.7395-0.7071-0.1166-0.63060.35330.15350.0010.51150.00510.3465-31.778556.35958.7109
291.97640.3373-0.76099.3175-2.76872.1301-0.22332.46021.0009-0.69870.5766-0.3479-1.59341.0698-0.44830.60090.04710.13191.04140.08570.7632-21.776756.61441.0872
306.1317-0.6983-5.76642.3581-0.0145.6264-1.12391.0163-1.1604-0.93090.59171.24921.0482-0.55640.43290.42580.0217-0.08960.5058-0.05780.7106-38.592748.82427.0849
315.65922.5070.33567.0609-2.53181.22821.873-1.12510.10250.9268-1.2193-0.54890.49531.8858-0.47041.1342-0.0299-0.40721.47330.04080.77521.447242.743423.1595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 273 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 11 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 19 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 28 )
7X-RAY DIFFRACTION7chain 'B' and (resid 29 through 41 )
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 56 )
10X-RAY DIFFRACTION10chain 'B' and (resid 57 through 63 )
11X-RAY DIFFRACTION11chain 'B' and (resid 64 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 83 )
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 90 )
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 99 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 9 )
16X-RAY DIFFRACTION16chain 'D' and (resid 3 through 103 )
17X-RAY DIFFRACTION17chain 'D' and (resid 104 through 212 )
18X-RAY DIFFRACTION18chain 'D' and (resid 213 through 273 )
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 11 )
20X-RAY DIFFRACTION20chain 'E' and (resid 12 through 19 )
21X-RAY DIFFRACTION21chain 'E' and (resid 20 through 28 )
22X-RAY DIFFRACTION22chain 'E' and (resid 29 through 35 )
23X-RAY DIFFRACTION23chain 'E' and (resid 36 through 41 )
24X-RAY DIFFRACTION24chain 'E' and (resid 42 through 51 )
25X-RAY DIFFRACTION25chain 'E' and (resid 52 through 56 )
26X-RAY DIFFRACTION26chain 'E' and (resid 57 through 71 )
27X-RAY DIFFRACTION27chain 'E' and (resid 72 through 77 )
28X-RAY DIFFRACTION28chain 'E' and (resid 78 through 83 )
29X-RAY DIFFRACTION29chain 'E' and (resid 84 through 90 )
30X-RAY DIFFRACTION30chain 'E' and (resid 91 through 99 )
31X-RAY DIFFRACTION31chain 'F' and (resid 1 through 9 )

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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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