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- PDB-9j4v: Structural basis for recognition of SARS-CoV-2 conserved nucleoca... -

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Basic information

Entry
Database: PDB / ID: 9j4v
TitleStructural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B alpha chain
  • Nucleoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HLA-B7 SARS-CoV-2 / Nuleocapside / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / regulation of interleukin-12 production / negative regulation of interferon-beta production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Maturation of nucleoprotein / poly(U) RNA binding ...: / response to host immune response / viral RNA genome packaging / regulation of interleukin-12 production / negative regulation of interferon-beta production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Maturation of nucleoprotein / poly(U) RNA binding / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / CD28 dependent PI3K/Akt signaling / detection of bacterium / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / VEGFR2 mediated vascular permeability / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / 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 / molecular condensate scaffold activity / 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 / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / DDX58/IFIH1-mediated induction of interferon-alpha/beta / 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 / RNA stem-loop binding / specific granule lumen / Interleukin-1 signaling / 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 / viral capsid / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / PIP3 activates AKT signaling / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / early endosome membrane / protein homotetramerization / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / amyloid fibril formation / adaptive immune response / Induction of Cell-Cell Fusion / intracellular iron ion homeostasis / Attachment and Entry / learning or memory
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / MHC class I, alpha chain, C-terminal ...Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / 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/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 / HLA class I histocompatibility antigen, B alpha chain / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsYuan, P. / Wu, D.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270995 China
National Natural Science Foundation of China (NSFC)32100985 China
CitationJournal: To Be Published
Title: Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Authors: Yuan, P. / Wu, D.C.
History
DepositionAug 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
E: Nucleoprotein
F: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,12310
Polymers90,5366
Non-polymers5874
Water7,026390
1
A: HLA class I histocompatibility antigen, B alpha chain
B: Beta-2-microglobulin
E: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7496
Polymers45,2683
Non-polymers4813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-18 kcal/mol
Surface area18940 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
F: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3744
Polymers45,2683
Non-polymers1061
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-14 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.135, 87.323, 157.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein HLA class I histocompatibility antigen, B alpha chain / Human leukocyte antigen B / HLA-B


Mass: 32093.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01889
#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 1295.464 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9

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Non-polymers , 4 types, 394 molecules

#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 HEPES (pH 7.5), 0.2 M ammonium acetate, and 24% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.98→36.34 Å / Num. obs: 69994 / % possible obs: 99.2 % / Redundancy: 13 % / Biso Wilson estimate: 34.38 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 6829 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→36.34 Å / SU ML: 0.2497 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.1912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2428 3512 5.04 %
Rwork0.2141 66127 -
obs0.2156 69639 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.56 Å2
Refinement stepCycle: LAST / Resolution: 1.98→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 36 390 6744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836572
X-RAY DIFFRACTIONf_angle_d0.93648925
X-RAY DIFFRACTIONf_chiral_restr0.0593890
X-RAY DIFFRACTIONf_plane_restr0.01431185
X-RAY DIFFRACTIONf_dihedral_angle_d7.208907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.010.38461270.32292415X-RAY DIFFRACTION91.97
2.01-2.030.35011460.31372613X-RAY DIFFRACTION99.39
2.03-2.060.26741430.28542632X-RAY DIFFRACTION99.75
2.06-2.10.2891400.29492584X-RAY DIFFRACTION99.05
2.1-2.130.31171370.27522643X-RAY DIFFRACTION99.5
2.13-2.170.32261180.2712632X-RAY DIFFRACTION99.78
2.17-2.210.2951200.26892628X-RAY DIFFRACTION99.42
2.21-2.250.28481530.26912661X-RAY DIFFRACTION99.5
2.25-2.30.32531460.27862562X-RAY DIFFRACTION99.12
2.3-2.350.3041360.2612644X-RAY DIFFRACTION99.71
2.35-2.40.32031410.25682661X-RAY DIFFRACTION99.54
2.4-2.460.27791500.25962621X-RAY DIFFRACTION99.75
2.46-2.530.28681200.24182613X-RAY DIFFRACTION99.45
2.53-2.60.27931570.24732649X-RAY DIFFRACTION99.68
2.6-2.690.27811360.24992663X-RAY DIFFRACTION99.75
2.69-2.780.28031430.2382647X-RAY DIFFRACTION99.57
2.78-2.890.2641450.25022649X-RAY DIFFRACTION99.64
2.89-3.020.29531320.24562664X-RAY DIFFRACTION99.61
3.02-3.180.30771160.22522674X-RAY DIFFRACTION99.79
3.18-3.380.23841620.21952664X-RAY DIFFRACTION99.86
3.38-3.640.22861490.19742684X-RAY DIFFRACTION99.68
3.64-4.010.18571440.17872687X-RAY DIFFRACTION99.72
4.01-4.590.18651590.1542698X-RAY DIFFRACTION99.69
4.59-5.780.1871400.15522742X-RAY DIFFRACTION99.48
5.78-36.340.20921520.18312797X-RAY DIFFRACTION96.82
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)
12.200909264370.5219499063610.04886068511990.488348047403-0.2411051243682.281981979630.0572448449437-0.212276227608-0.0235811520571-0.0934976527081-0.1312237401060.02251930943060.322568098765-0.0205044725647-0.0006699518488760.3106379489510.0571138793983-0.01586310495850.318616401459-0.0004769955989470.286277642252-16.040767002919.8741932767-52.7411453314
22.534861652851.298225697481.403681002751.880222122890.09268699655441.24414800678-0.3121378604220.610383328666-0.180861149896-0.108473073960.304458894263-0.153994630647-0.04018660089140.297469694595-0.01210911999010.287201959074-0.0504118217482-0.03353190800880.352259766406-0.05986609170860.336562354814-23.517979833111.4883396228-86.7679393446
30.04340147543080.0115655559977-0.06613788215880.3681167157370.08894441757610.889544270627-0.101484934534-0.1203119060710.0404010600182-0.6442215712840.207548902038-0.1291032224610.2696147533860.3873044857230.004977603864670.4273876371940.00417935686317-0.0453025631690.3432956685190.002634007119590.388523013403-11.440775331326.7708115869-74.8649430684
41.4402118091-0.315243175285-0.5118424855791.528726925650.5986438394252.56469211605-0.0676419976734-0.1427762783890.0744716311438-0.9641089750260.4653877328590.4039189929910.03514589931560.2128412074961.233769989090.564451854367-0.0553660192173-0.2952694910270.04586219959890.2241403196060.464736596696-22.883323837631.1001630291-76.8820514468
50.3695544953530.3962082875470.5039685027030.344907257118-0.1913587057270.628316863740.247132758093-0.03491857149020.414734101476-0.786152247277-0.2253563351450.1981277781380.7744072487230.2713876203420.003608747460820.4026284522390.0759983873177-0.04955856402020.3007674690780.05610955007620.508669022599-19.558796601431.3634231869-69.9731792315
60.772332310673-0.289526932327-0.3959139686490.592971964560.1589239232151.366390036240.05729451781690.06989047044720.513408185295-0.8376620988340.2532207734990.7681463874480.2081869824610.2928668280820.2606378066620.593273030116-0.0429794951386-0.2574955546570.05819234189470.1895139123330.662169350999-23.851181524133.9766059608-79.2939468948
70.885125912886-0.769281328606-0.8707370112040.8276419524980.6011059091841.04229196814-0.1069411966530.139345607743-0.259468110817-1.043060007330.2658670505830.0499358809420.130718197188-0.09361495711640.4066184158420.586605367412-0.0775300329236-0.1077171787260.335477225340.1473043627050.419937221328-14.740111555232.2356720659-82.7958192744
81.91934674931-0.5649629355490.2215721810110.294829238283-0.4285157768032.347010186550.08224221796360.183740745940.07811999843670.0867527775176-0.2259066943210.00438866848504-0.27037761944-0.000668147909738-0.008467318499010.278108800783-0.04156257910180.01355670472810.299517760115-0.000676917857920.262445526628-16.116113266222.8760921287-25.8230282979
91.71044293374-1.117257310830.05408994291131.801699313950.005851239139480.782811678344-0.310015037205-0.119506772076-0.07065479716130.1443630643940.229673020486-0.0591710476108-0.122906271025-0.0746534338731-0.000223290757490.3577767762240.03820372880120.05334575583980.270599792185-0.01305912417040.285153354758-23.159540308332.38560991828.06541927392
100.0283862906861-0.0844012148475-0.0287588976440.2855039725930.04511973551330.444864742817-0.2749570272040.100684493317-0.02596172554190.3682371405610.205514706688-0.0263366601396-0.3791535599750.389602851115-0.001171572464480.429476638273-0.0476918561710.02522978761610.3721562845140.01626026500130.326306904592-11.33298161616.4530956113-3.48280199111
111.490710521920.3288924427110.3118899465910.614884177367-0.03753255997791.42071481984-0.5027545266980.00994169120877-0.4765748733071.354738454910.3452110273390.2543075693730.132885157111-0.0723335258680.08274786908630.535144536590.0514487107310.4442119457910.2132373019570.1236967537450.473919207908-27.449816293415.21799436361.63522317778
121.267665058630.18324523788-0.08045135492850.36719403620.1690734779590.377596331007-0.3079050742810.386697411929-0.5622298235890.08577063660050.05816287796920.2053776497160.2011591275120.046427259452-0.01178728038230.430633212428-0.02992593541230.1602364709690.3107178644570.02438058498840.47394213582-19.63711677095.25015230429-3.67698414976
130.05795224846530.0226190933910.002480455262460.0136920348449-0.02643899513370.01749959713690.01094011373340.324777718484-0.26403210115-0.0227639914293-0.07720300017050.314008341718-0.3422658344390.1709907110150.0002740924021280.360477325763-0.0155310538278-0.008302390537090.313877184688-0.05399971803590.379655927352-18.728135119116.6779621369-14.7336003493
141.00998634332-0.886145307609-0.07042649757780.901295149302-0.3325497608874.091076256660.139081264379-0.3377420098470.004777308012830.892932998783-0.02384530481750.752036038822-1.070235628170.599776990263-0.1508255975140.4172118139160.03834135694430.2766549840550.1651768457440.004894745515240.472835772046-22.170972357613.9879344077-2.39834809517
150.1383242631470.05765171245790.04945782849010.1344034775290.07118443518820.761257904201-0.1377214235050.0103866262029-0.05665150264370.4308226111770.1965225635780.268586777648-0.01336505015710.3361378825110.009658058276430.454859061389-0.07400661453840.03440007142490.2762712792090.05847701220230.364564275499-11.36963953897.07214510604-0.0971478139837
160.685828885480.4497770276650.08878615220471.494296052211.502921332831.701584368720.143651703314-0.4663521391380.2052759868410.5142308499040.495353460088-0.0693906594066-0.105632829764-0.2829861804420.4672715526580.8084726383730.08950998539550.2503398730330.4003542657710.126607118030.336654982304-20.273842060413.98540825298.8808028006
170.0616288942321-0.02656973414530.01630453925620.166284110468-0.07078078733870.103678166608-0.1977572608490.379438491623-0.0276199900078-0.200180787014-0.0769876679198-0.02814067960830.3031179525270.2169454375660.0002019082346650.3410098193680.04841523657110.01297698736770.4721843041470.003645121555770.322145417389-14.642054148319.648613699-44.684840118
180.04989163300330.0465434802155-0.03088869121230.212025987252-0.08015980723080.100162954024-0.00781188374536-0.3948073909290.100180100633-0.144280373391-0.1273920422360.136303189694-0.2042478448930.267434510294-0.0001140119231240.3015462366840.0126870846113-0.01865312469880.4776267990230.01365901540990.305114442335-14.64644144622.9487289481-33.8957806048
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 180 )AA1 - 1801 - 180
22chain 'A' and (resid 181 through 275 )AA181 - 275181 - 275
33chain 'B' and (resid 0 through 11 )BF0 - 111 - 12
44chain 'B' and (resid 12 through 41 )BF12 - 4113 - 42
55chain 'B' and (resid 42 through 61 )BF42 - 6143 - 62
66chain 'B' and (resid 62 through 83 )BF62 - 8363 - 84
77chain 'B' and (resid 84 through 99 )BF84 - 9985 - 100
88chain 'C' and (resid 1 through 180 )CG1 - 1801 - 180
99chain 'C' and (resid 181 through 275 )CG181 - 275181 - 275
1010chain 'D' and (resid 0 through 11 )DH0 - 111 - 12
1111chain 'D' and (resid 12 through 30 )DH12 - 3013 - 31
1212chain 'D' and (resid 31 through 51 )DH31 - 5132 - 52
1313chain 'D' and (resid 52 through 56 )DH52 - 5653 - 57
1414chain 'D' and (resid 57 through 77 )DH57 - 7758 - 78
1515chain 'D' and (resid 78 through 90 )DH78 - 9079 - 91
1616chain 'D' and (resid 91 through 99 )DH91 - 9992 - 100
1717chain 'E' and (resid 1 through 9 )EI1 - 91 - 9
1818chain 'F' and (resid 1 through 9 )FJ1 - 91 - 9

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