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- PDB-3sv6: Crystal structure of NS3/4A protease in complex with Telaprevir -

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Basic information

Entry
Database: PDB / ID: 3sv6
TitleCrystal structure of NS3/4A protease in complex with Telaprevir
ComponentsNS3 protease, NS4A protein
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / drug resistance / drug design / Protease inhibitors / serine protease / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / viral nucleocapsid / 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 / induction by virus of host autophagy / ribonucleoprotein complex / viral RNA genome replication / cysteine-type endopeptidase activity / 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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / 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 non-structural protein NS2, C-terminal domain / Hepatitis C virus core protein, chain A superfamily ...Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / 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 non-structural protein NS2, C-terminal domain / 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 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 zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepatitis C virus, Non-structural protein NS2 / : / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus non-structural 5a protein membrane anchor / 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 / Hepacivirus/Pegivirus NS3 protease domain profile. / Hepatitis C virus NS3 protease / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Trypsin-like serine proteases / 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 / Thrombin, subunit H / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
TELAPREVIR, bound form / Chem-SV6 / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSchiffer, C.A. / Romano, K.P.
CitationJournal: Plos Pathog. / Year: 2012
Title: The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors.
Authors: Romano, K.P. / Ali, A. / Aydin, C. / Soumana, D. / Ozen, A. / Deveau, L.M. / Silver, C. / Cao, H. / Newton, A. / Petropoulos, C.J. / Huang, W. / Schiffer, C.A.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_molecule_features / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: NS3 protease, NS4A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4395
Polymers21,5031
Non-polymers9354
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.116, 58.850, 60.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NS3 protease, NS4A protein


Mass: 21503.330 Da / Num. of mol.: 1
Fragment: NS4A (UNP residues 1674-1688), NS3 (UNP residues 1027-1208)
Mutation: A1027S, P1028G, I1029D, L1039E, L1040E, I1043Q, I1044E, L1047Q, A1066T, C1073S, C1078L, I1098T, P1112Q, S1165A, C1185S, C1679S, V1686I, I1687N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Strain: subtype 1a, BID-V318 / Gene: NS3-NS4A / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8DG50

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-SV6 / (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide / TELAPREVIR, bound form


Type: peptide-like, Peptide-like / Class: Antiviral / Mass: 681.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H55N7O6 / References: TELAPREVIR, bound form / Comment: antivirus, protease inhibitor*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTELAPREVIR IS A LINEAR, PEPTIDOMIMETIC HCV NS3/4A PROTEASE INHIBITOR FROM VERTEX. TELAPREVIR WAS ...TELAPREVIR IS A LINEAR, PEPTIDOMIMETIC HCV NS3/4A PROTEASE INHIBITOR FROM VERTEX. TELAPREVIR WAS FDA APPROVED FOR CLINICAL USE IN HUMANS. THE DRUG MIMICS THE PEPTIDE BACKBONE OF PROTEINS, ALTHOUGH THE DRUG MOIETIES CANNOT BE SEQUENCED USING AMINO ACID NOMENCLATURE
Sequence detailsTHE COFACTOR 4A RESIDUES 986-1000 (MET LYS LYS LYS GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN ...THE COFACTOR 4A RESIDUES 986-1000 (MET LYS LYS LYS GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY CORRESPOND TO RESIDUES NUMBERING 1674-1688 OF DATABASE SEQUENCE REFERENCE (UNP A8DG50). THIS PEPTIDE IS COVALENTLY LINKED TO THE N-TERMINUS OF NS3. C1679S MUTATION WAS ENGINEERED TO PREVENT DISULFIDE FORMATION. THE V1686I AND I1687N WERE ENGINEERED TO OPTIMIZE THE LINKER BETWEEN THE COFACTOR 4A AND NS3.

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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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 295 K / Method: hanging drop, vapor diffusion / pH: 6.2
Details: 20-25% PEG 3350, 0.1M MES (pH 6.5), 4% ammonium sulfate, hanging drop, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorDate: Mar 31, 2001
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 39340 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.05 / Χ2: 1.001 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.455.50.476385211100
1.45-1.515.50.3539041.002199.9
1.51-1.585.60.25838861.0021100
1.58-1.665.60.17738671.001199.9
1.66-1.765.60.128389911100
1.76-1.95.70.08839240.9991100
1.9-2.095.60.066392411100
2.09-2.395.50.061395111100
2.39-3.025.50.05239971.0011100
3.02-505.30.02841361.002198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→33.47 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1817 / WRfactor Rwork: 0.1685 / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.9125 / SU B: 1.575 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0529 / SU Rfree: 0.0519 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1711 1959 5 %RANDOM
Rwork0.1578 ---
obs0.1584 39154 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.75 Å2 / Biso mean: 19.491 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2---0.76 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 61 167 1657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211545
X-RAY DIFFRACTIONr_bond_other_d0.0010.021002
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9882117
X-RAY DIFFRACTIONr_angle_other_deg0.8353.0072400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2622.70848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5115216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7831510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02297
X-RAY DIFFRACTIONr_mcbond_it0.6541.51018
X-RAY DIFFRACTIONr_mcbond_other0.1731.5422
X-RAY DIFFRACTIONr_mcangle_it1.19121633
X-RAY DIFFRACTIONr_scbond_it1.8383527
X-RAY DIFFRACTIONr_scangle_it2.8644.5478
LS refinement shellResolution: 1.4→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 137 -
Rwork0.212 2650 -
all-2787 -
obs--96.8 %
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)
125.955731.018213.875827.265519.56338.22770.9537-0.9916-0.49760.1557-1.23340.0511-2.6431-1.52890.27970.40430.11870.04230.1020.09990.22567.4098-23.9903-4.7249
20.83620.9086-1.26514.81430.22982.523-0.13840.0271-0.0337-0.31970.0673-0.11610.11380.07650.07120.08760.00370.01770.11410.01640.10414.9756-9.197112.0417
34.5801-0.3175-3.03640.1063-0.75344.7860.1193-0.49610.17690.250.0147-0.0366-0.7350.3474-0.1340.3759-0.05550.04080.1-0.01590.09920.54075.009427.8396
42.7456-0.7501-2.44312.94310.71654.65510.02-0.0980.01340.0622-0.04290.00990.0120.19750.02290.079-0.01140.01120.04810.01720.08674.20894.567418.7657
51.4161-1.15580.54964.1479-0.23964.7290.06020.04710.0638-0.436-0.092-0.3451-0.16330.17360.03180.09110.01110.0680.05120.01840.097610.7541-5.71159.5157
67.13791.3864-2.40171.42490.36421.86710.0213-0.16520.15610.05710.0454-0.0862-0.08210.1545-0.06670.0894-0.0311-0.00510.07230.00860.09026.3163-2.176124.2578
72.1336-0.9121.75289.09190.00454.78330.30110.3151-0.0126-0.6246-0.1041-0.07090.06830.0973-0.1970.1040.02960.00970.1313-0.00210.0779-0.4863-5.870711.1501
80.7391-0.1102-0.3860.58140.05060.35320.00780.056-0.03010.0159-0.0305-0.03750.00750.0120.02260.0750.00670.00290.07230.00290.0779-1.6325-12.03520.002
92.93221.46-0.87211.5584-1.33881.17150.0808-0.0434-0.1312-0.0421-0.1558-0.11280.07470.14910.0750.0690.01690.00770.08050.00520.11287.9142-16.211419.1519
100.82620.38780.15560.94880.36121.04660.04660.0546-0.09230.0561-0.0524-0.06040.02260.03730.00580.06490.00650.00330.06320.00040.093-0.2931-15.217822.7357
114.50510.5499-5.25781.63890.19836.2917-0.0286-0.3533-0.09990.089-0.0945-0.01150.08780.34680.12310.0593-0.00050.00270.14840.00770.0402-5.8869-8.898837.093
124.25861.6542-4.98040.6871-2.26778.58350.1587-0.30260.26120.0243-0.07180.067-0.10250.1242-0.08690.0811-0.00690.02270.0882-0.02540.1012-13.4374-1.514330.821
138.8724-0.2085-9.920111.17676.265825.4250.14850.15290.7741-0.18760.14840.2918-0.34350.3105-0.29690.06270.00030.03790.0180.03630.117-7.24654.147120.8456
142.97060.0712-0.52983.711-0.80451.30170.07950.06730.0540.0431-0.0274-0.0487-0.0013-0.0551-0.05210.0562-0.00080.02320.08520.00730.0722-19.1838-5.782829.9563
151.9976-1.4824-1.0427.1534-1.59691.45260.15340.22340.04590.0147-0.08150.0918-0.1408-0.1999-0.07190.08860.04030.02110.13810.01950.0698-21.2645-1.640625.1765
167.9538-5.6587-0.4977.7431-1.98441.31860.07830.07080.3750.26010.1349-0.0156-0.1897-0.1064-0.21320.09270.03810.03590.09630.03240.1021-14.19151.288916.5826
171.5801-0.0873-2.57570.73661.41736.65130.103-0.09530.160.01360.03410.0238-0.05260.1234-0.13710.0706-0.0080.01650.1023-0.01040.0841-8.5211-5.416331.6495
185.7615-1.10971.29726.5018-0.75480.2620.07090.31140.1895-0.1026-0.11340.23470.00760.05650.04250.080.0210.00340.1407-0.01020.0807-16.3267-8.040218.8726
192.21-0.60430.9811.15-1.36382.218-0.00940.0319-0.05580.00960.18480.1109-0.0327-0.2456-0.17540.06610.0020.02150.1030.02150.0714-18.0049-7.181321.8941
2013.0893-3.6686-4.28212.38820.00445.3446-0.2212-0.4284-0.5960.06740.03050.23990.42430.17740.19070.10950.02290.01050.04760.04430.094-5.6949-19.358331.4859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A980 - 987
2X-RAY DIFFRACTION2A988 - 996
3X-RAY DIFFRACTION3A997 - 1004
4X-RAY DIFFRACTION4A1005 - 1012
5X-RAY DIFFRACTION5A1013 - 1026
6X-RAY DIFFRACTION6A1027 - 1034
7X-RAY DIFFRACTION7A1035 - 1041
8X-RAY DIFFRACTION8A1042 - 1063
9X-RAY DIFFRACTION9A1064 - 1076
10X-RAY DIFFRACTION10A1077 - 1092
11X-RAY DIFFRACTION11A1093 - 1100
12X-RAY DIFFRACTION12A1101 - 1108
13X-RAY DIFFRACTION13A1109 - 1113
14X-RAY DIFFRACTION14A1114 - 1122
15X-RAY DIFFRACTION15A1123 - 1129
16X-RAY DIFFRACTION16A1130 - 1139
17X-RAY DIFFRACTION17A1140 - 1153
18X-RAY DIFFRACTION18A1154 - 1159
19X-RAY DIFFRACTION19A1160 - 1172
20X-RAY DIFFRACTION20A1173 - 1180

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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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