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- PDB-6v80: Crystal structure of human CD1d presenting alpha-Galactosylcerami... -

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Basic information

Entry
Database: PDB / ID: 6v80
TitleCrystal structure of human CD1d presenting alpha-Galactosylceramide in complex with NKT12 TCR and VHH nanobody 1D12
Components
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
  • Nanobody VHH ID12
  • T cell receptor alpha variable 10, nkt tcr alpha chain fusion
  • nkt tcr beta chain
KeywordsIMMUNE SYSTEM / lipid / nanobody
Function / homology
Function and homology information


lipid antigen binding / T cell selection / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of innate immune response / heterotypic cell-cell adhesion / T cell receptor complex ...lipid antigen binding / T cell selection / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of innate immune response / heterotypic cell-cell adhesion / T cell receptor complex / beta-2-microglobulin binding / detection of bacterium / positive regulation of T cell proliferation / cell adhesion molecule binding / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / 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 / ER to Golgi transport vesicle membrane / 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 / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / iron ion transport / ER-Phagosome pathway / early endosome membrane / histone binding / T cell differentiation in thymus / protein refolding / basolateral plasma membrane / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / lysosome / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
T-cell receptor alpha chain, constant domain / MHC-I family domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain ...T-cell receptor alpha chain, constant domain / MHC-I family domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Chem-AGH / T cell receptor alpha variable 10 / Human nkt tcr alpha chain / Human nkt tcr beta chain / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 Å
AuthorsShahine, A. / Rossjohn, J.
CitationJournal: Nat Cancer / Year: 2020
Title: A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.
Authors: Shahine, A. / Rossjohn, J.
History
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
C: T cell receptor alpha variable 10, nkt tcr alpha chain fusion
D: nkt tcr beta chain
E: Nanobody VHH ID12
F: Antigen-presenting glycoprotein CD1d
G: Beta-2-microglobulin
H: T cell receptor alpha variable 10, nkt tcr alpha chain fusion
I: nkt tcr beta chain
J: Nanobody VHH ID12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,22716
Polymers230,21910
Non-polymers3,0086
Water00
1
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
C: T cell receptor alpha variable 10, nkt tcr alpha chain fusion
D: nkt tcr beta chain
E: Nanobody VHH ID12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3927
Polymers115,1105
Non-polymers1,2832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-68 kcal/mol
Surface area45180 Å2
MethodPISA
2
F: Antigen-presenting glycoprotein CD1d
G: Beta-2-microglobulin
H: T cell receptor alpha variable 10, nkt tcr alpha chain fusion
I: nkt tcr beta chain
J: Nanobody VHH ID12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8359
Polymers115,1105
Non-polymers1,7254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-64 kcal/mol
Surface area45560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.667, 165.250, 84.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...
21(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGARGARG(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB34
12ASNASNASNASN(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB2122
13ILEILEMETMET(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB1 - 992 - 100
14ILEILEMETMET(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB1 - 992 - 100
15ILEILEMETMET(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB1 - 992 - 100
16ILEILEMETMET(CHAIN B AND (RESID 3 THROUGH 20 OR (RESID 21...BB1 - 992 - 100
21ARGARGARGARG(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...GG34
22GLNGLNASPASP(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...GG2 - 983 - 99
23GLNGLNASPASP(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...GG2 - 983 - 99
24GLNGLNASPASP(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...GG2 - 983 - 99
25GLNGLNASPASP(CHAIN G AND ((RESID 3 AND (NAME N OR NAME...GG2 - 983 - 99

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Components

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Protein , 4 types, 8 molecules AFBGCHDI

#1: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 39471.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Plasmid: pFastBac / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15813
#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: pFastBac / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769
#3: Protein T cell receptor alpha variable 10, nkt tcr alpha chain fusion


Mass: 23365.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV10, B2M, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4J240, UniProt: K7N5M3
#4: Protein nkt tcr beta chain


Mass: 27491.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K7N5M4

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Antibody , 1 types, 2 molecules EJ

#5: Antibody Nanobody VHH ID12


Mass: 12901.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMEK219 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1

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Sugars , 3 types, 6 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-AGH / N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE


Type: D-saccharide / Mass: 858.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C50H99NO9
#8: 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.: 2
Source method: isolated from a genetically manipulated source
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

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Details

Has ligand of interestN

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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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 21 % (v/v) PEG 3350, 0.2 M tri-sodium citrate, 3% (v/v) D-(+)-trehalose dehydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.39
ReflectionResolution: 3.53→82.82 Å / Num. obs: 35574 / % possible obs: 100 % / Redundancy: 15.2 % / CC1/2: 0.988 / Rpim(I) all: 0.117 / Net I/σ(I): 6
Reflection shellResolution: 3.53→3.7 Å / Redundancy: 15.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4684 / CC1/2: 0.462 / Rpim(I) all: 0.729 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PO6, 3P0G

2po6

3p0g


Resolution: 3.53→82.63 Å / Cross valid method: THROUGHOUT / σ(F): 246.34 / Phase error: 38.96 / Details: TWIN LAW: -H,-K,L
RfactorNum. reflection% reflection
Rfree0.254 1873 5.27 %
Rwork0.195 33582 -
obs0.206 35558 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 358.06 Å2 / Biso mean: 120.3 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.53→82.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14001 0 181 0 14182
Biso mean--107.33 --
Num. residues----1827
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B742X-RAY DIFFRACTIONPOSITIONAL0
12G742X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5322-3.62760.34921410.29062544268595
3.6276-3.73430.33121410.28762557269895
3.7343-3.85470.27031460.26622611275795
3.8547-3.99230.27341390.26782559269895
3.9923-4.15190.29331380.2462593273195
4.1519-4.34050.27731500.22562540269094
4.3405-4.56890.26631380.20752584272295
4.5689-4.85440.23541550.19832589274494
4.8544-5.22810.22171450.19122576272195
5.2281-5.75210.24411590.19252570272994
5.7521-6.57970.26281320.20372627275995
6.5797-8.27160.26991360.16682593272995
8.2716-35.00640.24071530.14642639279295
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)
11.6694-0.78370.87825.0119-3.23997.46890.4692-0.35050.0978-0.27480.08610.37790.58310.0576-0.47570.3243-0.0404-0.01620.5815-0.09210.794147.730317.304263.8169
24.2786-0.64092.62544.3211-2.19975.78750.38070.05720.2773-0.6718-0.34490.12571.03250.34190.06150.71760.01170.16510.45510.03191.03919.9484-8.928760.6842
35.8393-0.5625-2.67431.55270.11373.4075-0.0243-0.09690.54120.16440.12930.61810.3492-0.2966-0.06250.5727-0.0523-0.06290.57350.0711.143919.2813.251263.921
44.2323-0.87691.24233.13451.37514.1152-0.0153-0.5262-0.04180.5179-0.0606-0.27520.57070.00890.10410.4946-0.03860.00940.64090.17820.683972.017441.011268.4353
53.7065-0.9825-0.09223.73690.19724.6461-0.5524-0.25070.4686-0.21780.2137-0.0628-0.12920.11230.49850.8205-0.27680.05180.88480.01850.74188.911170.614869.4151
65.98740.90331.07185.1184-0.2276.037-0.6877-0.23391.0399-0.1982-0.173-0.3865-0.1960.01420.75060.695-0.0177-0.23290.58020.07571.048259.052451.169352.1682
71.5075-0.0785-0.36570.6334-1.05511.63250.0737-0.1710.8357-0.14330.01080.5888-0.1167-0.2078-0.10990.8383-0.1187-0.03660.577-0.14081.166681.930272.139352.6299
83.50830.67330.37941.8128-0.922.5633-0.1033-0.21720.9735-0.68670.074-0.56561.22311.1671-0.09810.60880.23630.02331.10430.2181.210477.080215.672478.5104
90.31590.0461-0.46470.08590.2130.64870.27820.06580.1758-0.5628-0.26220.54090.8921-0.56640.23910.8245-0.1687-0.15381.4079-0.09041.638615.544634.6226105.8255
105.0382-0.7853-0.54371.9537-0.42653.81990.12270.3553-0.5215-0.1961-0.1004-0.8895-0.0836-0.0697-0.00770.51990.03730.00250.47220.17531.301675.076926.6369100.8838
114.11290.86081.27915.1325-0.42823.5593-0.19511.37140.8303-0.93340.3821-0.71731.16320.6986-0.13390.89350.30690.03221.18-0.20591.031799.47062.595898.0645
125.0769-0.9544-0.38458.8432-2.04024.82810.01120.0113-0.45390.739-0.0483-0.0002-0.3177-0.2651-0.02220.3731-0.0803-0.09880.59830.07180.625165.163913.3211116.9925
133.11110.45940.16892.9429-0.93771.77940.33820.01230.0333-0.0297-0.13820.36330.42870.5327-0.17650.60540.1515-0.08510.7853-0.03071.432691.5852-0.9525114.4375
142.10370.2015-0.15342.77870.58493.72960.87910.10790.44830.2575-0.05820.1921-1.12440.1943-0.84011.0653-0.13260.18920.49520.17060.969269.812152.827590.4407
152.5535-1.0039-1.02683.6891-0.93916.13710.20850.463-0.44250.06220.39290.588-0.46-0.7233-0.4810.259-0.0084-0.03060.59480.01630.972843.319539.315106.6572
160.2335-0.5049-0.52381.18091.03490.06590.51850.246-0.95310.5079-0.85350.101-1.5761-0.65830.2530.91660.3665-0.00851.32070.20181.867214.459755.4378107.2883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 178 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 179 THROUGH 279 )A0
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 1 THROUGH 99 )B0
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 4 THROUGH 108 )C0
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 109 THROUGH 205 )C0
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 1 THROUGH 112 )D0
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 113 THROUGH 241 )D0
8X-RAY DIFFRACTION8CHAIN 'E' AND (RESID 1 THROUGH 118 )E0
9X-RAY DIFFRACTION9CHAIN 'G' AND (RESID 2 THROUGH 98 )G0
10X-RAY DIFFRACTION10CHAIN 'H' AND (RESID 4 THROUGH 114 )H0
11X-RAY DIFFRACTION11CHAIN 'H' AND (RESID 115 THROUGH 196 )H0
12X-RAY DIFFRACTION12CHAIN 'I' AND (RESID 1 THROUGH 104 )I0
13X-RAY DIFFRACTION13CHAIN 'I' AND (RESID 105 THROUGH 237 )I0
14X-RAY DIFFRACTION14CHAIN 'J' AND (RESID 1 THROUGH 119 )J0
15X-RAY DIFFRACTION15CHAIN 'F' AND (RESID 7 THROUGH 159 )F0
16X-RAY DIFFRACTION16CHAIN 'F' AND (RESID 160 THROUGH 278 )F0

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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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