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- PDB-7jtg: Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from... -

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Basic information

Entry
Database: PDB / ID: 7jtg
TitleStructure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody RM11-43
Components
  • Envelope glycoprotein E2
  • RM11-43 Fab heavy chain
  • RM11-43 Fab light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HCV / broadly neutralizing antibodies / bNAbs / E2 core / IGHV1-69 / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : ...Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesMacaca mulatta (Rhesus monkey)
Recombinant Hepatitis C virus HK6a/JFH-1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTzarum, N. / Wilson, I.A. / Law, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al123365 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al106005 United States
CitationJournal: Immunity / Year: 2021
Title: HCV Env immunization elicits a rapid VH1-69-like broadly neutralizing antibody response in rhesus macaques
Authors: Tzarum, N. / Chen, F. / Lin, X. / Giang, E. / Velazquez-Moctezuma, R. / Augestad, E.H. / Nagy, K. / He, L. / Davidson, E. / Chavez, D. / Prentoe, J. / Stanfield, R.L. / Lanford, R. / Bukh, J. ...Authors: Tzarum, N. / Chen, F. / Lin, X. / Giang, E. / Velazquez-Moctezuma, R. / Augestad, E.H. / Nagy, K. / He, L. / Davidson, E. / Chavez, D. / Prentoe, J. / Stanfield, R.L. / Lanford, R. / Bukh, J. / Wilson, I.A. / Zhu, J. / Law, M.
History
DepositionAug 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 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: RM11-43 Fab heavy chain
B: RM11-43 Fab light chain
E: Envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9095
Polymers68,2643
Non-polymers6462
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-28 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.956, 65.343, 215.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody RM11-43 Fab heavy chain


Mass: 24301.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody RM11-43 Fab light chain


Mass: 23254.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 47 molecules E

#3: Protein Envelope glycoprotein E2


Mass: 20707.395 Da / Num. of mol.: 1 / Mutation: N448D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Recombinant Hepatitis C virus HK6a/JFH-1
Production host: Homo sapiens (human) / References: UniProt: B9V0E2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 1
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
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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 20% (w/v) PEG 3350, 0.2M sodium sulfate, pH 6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 26778 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 64.18 Å2 / CC1/2: 0.92 / Net I/σ(I): 14.8
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 1146 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BKB

6bkb


Resolution: 2.6→29.75 Å / SU ML: 0.473 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.3991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2692 1367 5.12 %
Rwork0.2223 25348 -
obs0.2248 26715 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.94 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4429 0 42 46 4517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424577
X-RAY DIFFRACTIONf_angle_d0.80416227
X-RAY DIFFRACTIONf_chiral_restr0.0483714
X-RAY DIFFRACTIONf_plane_restr0.005785
X-RAY DIFFRACTIONf_dihedral_angle_d15.3972634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.45831140.37282221X-RAY DIFFRACTION88.35
2.69-2.80.34921460.31972487X-RAY DIFFRACTION99.81
2.8-2.920.37131220.28962541X-RAY DIFFRACTION99.96
2.92-3.080.341170.28232557X-RAY DIFFRACTION100
3.08-3.270.32831250.2812559X-RAY DIFFRACTION100
3.27-3.520.33591290.24742552X-RAY DIFFRACTION99.96
3.52-3.880.25211420.22442552X-RAY DIFFRACTION100
3.88-4.440.24631440.18792561X-RAY DIFFRACTION100
4.44-5.580.20391630.16892590X-RAY DIFFRACTION99.96
5.58-29.750.25541650.20612728X-RAY DIFFRACTION99.97
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)
11.480564387191.95146624322-2.474408409454.59898303247-4.696714216285.273946960550.680391389542-0.1940068580540.6408864696990.950804789104-0.1875877035550.53587672715-1.95018143826-0.398776902265-0.5303095420330.6743543354490.0754558563439-0.01561201805940.596771181524-0.09117444183980.565020255604-10.03259108663.1411182348367.9934288369
21.336232764120.5439535624150.962337406973.02235605136-0.9368804074423.35660727041-0.1146565085280.1157588641350.0208066156955-0.0714805079110.0590322048346-0.165431961716-0.2599922285970.1730609312540.09871848959070.567790103858-0.078219057114-0.02286233683370.444604823656-0.004054125367350.451493611551-0.830452787247-1.8050707457973.9145211005
31.742100342320.264411835966-0.298795152532.73005359814-0.4314401259472.42106054531-0.205901464997-0.178183661314-0.373317708827-0.273495221424-0.3423736709950.121807465141-1.724388311350.4239758935610.9123066380460.6663440298340.00390149759752-0.05419278143070.355644137739-0.01516723686590.533200757192-2.660416903734.6474837434969.4485486508
43.254485075530.222615658838-0.2754299888612.272793159731.310477393820.8536409223330.0861389017451-0.443184101913-0.51590296898-0.1415459512180.1345565578030.517860652029-0.24902462265-0.246409576355-0.3021290891390.491197625331-0.116609010049-0.0126367761810.436320571145-0.005021724311180.604796046128-3.25719001468-7.8252324521778.2470507262
52.801852621340.7474879143241.800792940082.69082604732.090343251172.88238680382-0.183949293441-0.359495195757-0.001846736093960.1878440187230.1344900229860.3789370118510.309081296511-1.087978033290.03596778786280.539379956294-0.08060565796770.08711722798340.453768910296-0.1047611889050.554641318769-7.32777886174-8.372557546676.1934774892
60.2104776113130.576519156290.03181171230262.09923952566-1.030298997513.265236297370.0803306490115-0.1384847975040.056263417180.248776164259-0.2295301433640.794080342006-0.694020966093-0.8224697944880.1441316476930.432888504930.2282177440690.02690620285710.65055845601-0.174796715890.717994581956-25.364537321-5.0116252722344.6869956815
74.61261176873-1.555919773391.360354776962.765394108780.6511005098652.81998079926-0.2917291556760.000538752982716-0.5992143215190.211702180460.2036056739020.2412058885560.7374562864470.05042059378420.004996778714730.636586764648-0.1901933065960.01631449067450.4332390323610.01646562162230.412494826168-1.24562791733-24.127612960368.3165965934
81.73341795196-0.6488549340070.6972008275272.345138541320.4544716944332.699007613020.144969828926-0.5495017794-0.4970525973750.163779740654-0.1520617697120.4157984783720.920698712225-0.699214632701-0.01618939811080.705422314373-0.236507698719-0.00293316307870.5894656761910.05774866561620.53525044522-8.72234126543-23.352402062372.5666278818
90.208007632961-0.698634566123-0.2191402087973.40035137343-0.4630772277622.24920401420.02891713509310.213206104744-0.7512738302610.866077004410.109940101457-0.803436797916-0.02133975518970.2406653068880.09566500284410.383466636634-0.194164850199-0.05028585133090.4568648301330.01542985517550.4721094520723.43892950855-15.020056483371.329611944
101.20250228830.1680863799822.322432760170.4249229555921.144262928276.121389610540.521928927602-0.281479459294-0.1840294611380.4162855316830.199337680543-0.09045170253830.6830538020460.167604827251-0.6870665034650.771839708894-0.2616820824840.01579089602020.665692692482-0.07211441976820.456839188802-16.92416059-28.865380114852.7025458548
113.425879081531.368339385720.1644264046865.668476513780.6157738131113.489604229290.183588478940.186172353890.667503100258-0.635417471239-0.2587199969231.12436890189-1.42575604615-1.044682647440.05480592985760.7081547849490.37433971968-0.1551424795620.717465288702-0.1287659057570.581385271198-22.152967521-6.6834574954332.7783936841
121.004242132751.64486011305-0.9466919457786.79310776115-4.072858231486.810783171780.07791113045170.081115702601-0.219891605518-0.216730102352-0.0389563615612-0.04643563329630.3524458701530.1693090894920.2670206392530.3289665853960.0259230999683-0.03276571328940.473857289343-0.05237473746150.616100980831-15.2273365446-18.603626834539.4022901833
132.294450736121.148189728150.1225101361825.49257143721-0.8756136518786.39186477825-0.06985553662850.0997056209889-0.3201681934640.204034986716-0.193358811611-0.411747068452-0.240876032288-0.6145650345880.2258018395730.3026871813480.002724776409980.02963226536290.482072936187-0.07357209060540.584819229978-14.8877322014-17.694602120843.4272193895
142.628663781121.6056668628-0.3790647001636.18823647548-0.140760783734.32572818689-0.04588332991540.3501339649040.00675250519414-1.25986674765-0.451384664755-0.448618613182-0.233995636707-0.1035207240010.1791508189210.5470978913450.178551514091-0.06463870532190.520246087548-0.04208040482890.461645495414-15.6744152777-15.321526287930.2811681731
155.86852542094-1.18452278245-0.2319359981583.53873079307-0.7642426146775.03263846383-0.443320350271-0.1298715938240.424829264575-0.03321468231630.6188303335350.0617645311055-0.01500725028830.515646297448-0.2677895038470.702766554867-0.109352247035-0.03607536863460.675190395813-0.06585197655650.4767989734134.68569819832-0.22842512031494.405204934
162.29888606021-2.3858484221-1.998225428855.391469721990.4847917446075.28868361310.3535415586111.536780007260.205097059271-0.95670601790.184378832984-1.06965823860.3053695617230.710701818037-0.07490763907750.952340830581-0.17615342964-0.03337327559870.772584205617-0.07224238169440.83270127162414.7155784022-5.7406439281486.0107695354
173.567157528620.42899272535-0.7340370048955.27855155867-0.400482053844.097718622780.111943320987-0.565812284550.4586951507510.828871899191-0.128838631810.112131297481-1.01318662823-0.111372966463-0.04429451536430.802380048537-0.117512060052-0.01426728362330.794187882653-0.0572817947670.4761475994243.84910726758-5.39196590456105.39489115
184.26327163444-2.909131445160.7771744914234.53499695956-1.189806734072.899584160020.0638196290702-1.67520575088-0.02643558488380.512671776041-0.0884323340145-0.3785731753150.4060319521470.608073048609-0.07063890553220.809012869817-0.1214144393080.06753749540711.100564165850.03819715018580.591286442379.43988326734-9.57863130501108.582141727
193.68668065268-2.157206146330.3929024276233.7436392288-0.5783912343414.143618958370.254466778950.0257358378919-0.3941525908280.176167363899-0.1525720898410.1054608958350.5145614025280.52972103635-0.1008628225240.639401026764-0.133457815167-0.08939807505720.84589564766-0.006143879087660.63430504152817.3713333915-16.153502587998.6478211168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 100A)
5X-RAY DIFFRACTION5chain 'A' and (resid 100B through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 214 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 38 )
8X-RAY DIFFRACTION8chain 'B' and (resid 39 through 90 )
9X-RAY DIFFRACTION9chain 'B' and (resid 91 through 102 )
10X-RAY DIFFRACTION10chain 'B' and (resid 103 through 113 )
11X-RAY DIFFRACTION11chain 'B' and (resid 114 through 128 )
12X-RAY DIFFRACTION12chain 'B' and (resid 129 through 150 )
13X-RAY DIFFRACTION13chain 'B' and (resid 151 through 174 )
14X-RAY DIFFRACTION14chain 'B' and (resid 175 through 212 )
15X-RAY DIFFRACTION15chain 'E' and (resid 421 through 436 )
16X-RAY DIFFRACTION16chain 'E' and (resid 437 through 452 )
17X-RAY DIFFRACTION17chain 'E' and (resid 453 through 535 )
18X-RAY DIFFRACTION18chain 'E' and (resid 536 through 555 )
19X-RAY DIFFRACTION19chain 'E' and (resid 556 through 645 )

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