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- PDB-5n0a: Crystal structure of A259C covalently linked dengue 2 virus envel... -

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Basic information

Entry
Database: PDB / ID: 5n0a
TitleCrystal structure of A259C covalently linked dengue 2 virus envelope glycoprotein dimer in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 A11
Components
  • BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11
  • BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 HEAVY CHAIN
  • Envelope Glycoprotein E
KeywordsImmune System/Viral protein / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / DENGUE VIRUS / ENVELOPE FUSION PROTEIN / BROADLY NEUTRALIZING ANTIBODY
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsVaney, M.C. / Rouvinski, A. / Guardado-Calvo, P. / Sharma, A. / Rey, F.A.
Citation
Journal: Nat Commun / Year: 2017
Title: Covalently linked dengue virus envelope glycoprotein dimers reduce exposure of the immunodominant fusion loop epitope.
Authors: Rouvinski, A. / Dejnirattisai, W. / Guardado-Calvo, P. / Vaney, M.C. / Sharma, A. / Duquerroy, S. / Supasa, P. / Wongwiwat, W. / Haouz, A. / Barba-Spaeth, G. / Mongkolsapaya, J. / Rey, F.A. / Screaton, G.R.
#1: Journal: Nature / Year: 2015
Title: Recognition determinants of broadly neutralizing human antibodies against dengue viruses.
Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. ...Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / Petres, S. / Shepard, W.E. / Despres, P. / Arenzana-Seisdedos, F. / Dussart, P. / Mongkolsapaya, J. / Screaton, G.R. / Rey, F.A.
History
DepositionFeb 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope Glycoprotein E
B: Envelope Glycoprotein E
H: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 HEAVY CHAIN
I: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 HEAVY CHAIN
L: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11
M: BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,9958
Polymers201,8816
Non-polymers2,1142
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13660 Å2
ΔGint9 kcal/mol
Surface area54130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.774, 182.301, 208.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Envelope Glycoprotein E


Mass: 47477.172 Da / Num. of mol.: 2 / Mutation: A259C
Source method: isolated from a genetically manipulated source
Details: The SOLUBLE ECTODOMAIN of envelope glycoprotein E is mutated at position 259: Ala is replaced by Cys.
Source: (gene. exp.) Dengue virus 2 / Variant: FGA-02 / Plasmid: PMT/BIP/V5-HIS / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q68Y26, UniProt: A0A0B4SHY9*PLUS
#2: Antibody BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11 HEAVY CHAIN


Mass: 30355.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FAB FRAGMENT HEAVY CHAIN, RESIDUES 1-263. The residues numbering is the KABAT scheme numbering.
Source: (gene. exp.) Homo sapiens (human) / Cell: B LYMPHOCYTE / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11


Mass: 23107.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FAB FRAGMENT LIGHT CHAIN, RESIDUES 1-213. The residues numbering is the KABAT scheme numbering.
Source: (gene. exp.) Homo sapiens (human) / Cell: B LYMPHOCYTE / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Hepes pH 7.5, 19% PEG 6K, 1.5% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2015
RadiationMonochromator: cryogenically cooled channel-cut Si[111] monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 19112 / % possible obs: 96.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 44.52 Å2 / Rmerge(I) obs: 0.316 / Rpim(I) all: 0.257 / Rrim(I) all: 0.41 / Rsym value: 0.316 / Net I/σ(I): 3.1
Reflection shellResolution: 3.9→4.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4789 / CC1/2: 0.68 / Rpim(I) all: 0.67 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTA;4UT7

4uta

4ut7


Resolution: 3.9→20 Å / Cor.coef. Fo:Fc: 0.7623 / Cor.coef. Fo:Fc free: 0.7118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.85
Details: BUSTER/TNT refinement was used with TLS and NCS resraints
RfactorNum. reflection% reflectionSelection details
Rfree0.3 947 4.96 %RANDOM
Rwork0.2854 ---
obs0.2861 19112 90.67 %-
Displacement parametersBiso mean: 145.06 Å2
Baniso -1Baniso -2Baniso -3
1-9.7707 Å20 Å20 Å2
2---67.7068 Å20 Å2
3---57.9362 Å2
Refine analyzeLuzzati coordinate error obs: 0.858 Å
Refinement stepCycle: 1 / Resolution: 3.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9701 0 142 0 9843
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00710076HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1313672HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3498SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1439HARMONIC5
X-RAY DIFFRACTIONt_it10076HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion20.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1366SEMIHARMONIC5
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_contact10691SEMIHARMONIC4
LS refinement shellResolution: 3.9→4.11 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3097 118 5.15 %
Rwork0.2726 2173 -
all0.2746 2291 -
obs--76.21 %
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)
15.60331.00870.74090-2.91041.5754-0.02960.11630.0027-0.1398-0.07040.04490.05980.10930.1-0.30390.07230.0030.27070.1228-0.0539-29.786111.0143-59.0007
24.80582.12342.909301.35161.33680.0318-0.21460.3757-0.18950.2503-0.19160.10110.1808-0.282-0.30380.0186-0.06250.1315-0.13290.2752-5.386315.6791-18.1222
33.5794-2.9104-2.85920.0003-2.84691.2889-0.03880.06570.0059-0.30910.0350.13160.25050.01610.0038-0.177-0.1519-0.1520.04820.13790.223-26.563716.6614-85.5382
40-0.7779-2.596701.78050-0.0273-0.04270.06360.00930.050.1044-0.1505-0.0175-0.0226-0.19090.10830.08290.3033-0.1520.164131.024613.6861-4.4076
55.2162-2.07542.90990-1.54185.0833-0.0145-0.155-0.1826-0.1217-0.15330.0417-0.0569-0.04640.1678-0.30360.1423-0.0733-0.01540.1520.30386.840214.9173-45.2394
63.54492.0688-2.853702.36510.2588-0.0734-0.0908-0.04490.20910.1542-0.0930.29280.093-0.0808-0.30390.0586-0.1440.1219-0.15190.293928.034120.098922.1822
71.0058-0.75280.92441.13280.191700.00010.02060.05630.00320.02070.0278-0.0514-0.0001-0.0208-0.09-0.02-0.07260.13910.15190.188-24.53735.0355-69.5392
81.2791.05420.37670.47430.12200.00240.024-0.0353-0.0045-0.0085-0.02970.04530.00140.0061-0.0475-0.107-0.03280.0644-0.14190.174925.376737.78315.7016
91.02830.0471-0.01230.26260.24370.26710.15030.0352-0.1934-0.27150.01040.3587-0.42490.0105-0.1607-0.0227-0.0365-0.10750.3021-0.12260.12239.431946.4738-2.173
1000.7405-0.97860.1534-0.28811.41350.00760.121-0.20930.1178-0.2013-0.1767-0.3285-0.05990.1938-0.0342-0.0128-0.14860.2670.1520.1678-9.312644.3352-61.3218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1:52 131:193 270:293}
2X-RAY DIFFRACTION2{A|53:130 194:269}
3X-RAY DIFFRACTION3{A|294:393}
4X-RAY DIFFRACTION4{B|1:52 131:193 270:293}
5X-RAY DIFFRACTION5{B|53:130 194:269}
6X-RAY DIFFRACTION6{B|294:393}
7X-RAY DIFFRACTION7{A|501:506}
8X-RAY DIFFRACTION8{B|501:506}
9X-RAY DIFFRACTION9{H|1:132 L|1:113}
10X-RAY DIFFRACTION10{I|1:132 M|1:113}

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