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- PDB-5t9y: Crystal structure of the infectious salmon anemia virus (ISAV) he... -

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Basic information

Entry
Database: PDB / ID: 5t9y
TitleCrystal structure of the infectious salmon anemia virus (ISAV) hemagglutinin-esterase protein
ComponentsHE protein
KeywordsVIRAL PROTEIN / 4-0-acetylsialic acid / hydrolase / hemagglutinin / coiled-coil / viral receptor-complex / infectious salmon anemia virus / ISAV
Function / homologyHaemagglutinin-esterase glycoprotein, infectious salmon anaemia virus-type / Infectious salmon anaemia virus haemagglutinin / metal ion binding / membrane / FORMIC ACID / HE protein
Function and homology information
Biological speciesInfectious salmon anemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.8 Å
AuthorsCook, J.D. / Sultana, A. / Lee, J.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN 435607-13 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of the infectious salmon anemia virus receptor complex illustrates a unique binding strategy for attachment.
Authors: Cook, J.D. / Sultana, A. / Lee, J.E.
History
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HE protein
B: HE protein
C: HE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,52333
Polymers112,5863
Non-polymers2,93830
Water21,3841187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-63 kcal/mol
Surface area35760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.419, 93.289, 96.722
Angle α, β, γ (deg.)90.00, 122.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-832-

HOH

21B-898-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein HE protein / Hemagglutinin / Hemagglutinin-esterase glycoprotein


Mass: 37528.578 Da / Num. of mol.: 3 / Fragment: UNP residues 17-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious salmon anemia virus / Gene: HE / Plasmid: pMT-puro / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9J0Y0

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Non-polymers , 5 types, 1217 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1187 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: [0.2 M] magnesium formate, 20% PEG 3350, w/ a [0.8 M] sodium phosphate, [0.8 M] potassium phosphate, [0.1 M] HEPES pH 7.5 solution as a 1:6 ratio drop additive

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 28, 2016 / Details: 9 CCDS, 9 TILED FIBER-OPTIC TAPERS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→47.72 Å / Num. obs: 99190 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 21.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.8-1.834.20.4980.8461100
9.86-47.723.90.0290.998198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.77 Å47.61 Å
Translation7.77 Å47.61 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimless0.5.17data scaling
Cootmodel building
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASER2.6.0phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→47.72 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1677 2000 2.02 %Random selection
Rwork0.1367 ---
obs0.1373 99183 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7276 0 100 1187 8563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097605
X-RAY DIFFRACTIONf_angle_d0.98810330
X-RAY DIFFRACTIONf_dihedral_angle_d12.0864596
X-RAY DIFFRACTIONf_chiral_restr0.0611197
X-RAY DIFFRACTIONf_plane_restr0.0071332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.2231420.19356917X-RAY DIFFRACTION100
1.845-1.89490.18291430.17396958X-RAY DIFFRACTION100
1.8949-1.95070.19391420.1596879X-RAY DIFFRACTION100
1.9507-2.01360.19181430.14936944X-RAY DIFFRACTION100
2.0136-2.08560.1711410.14786889X-RAY DIFFRACTION100
2.0856-2.16910.15071440.13476941X-RAY DIFFRACTION100
2.1691-2.26780.17121420.13296908X-RAY DIFFRACTION100
2.2678-2.38740.13891420.136915X-RAY DIFFRACTION100
2.3874-2.5370.16171440.12996975X-RAY DIFFRACTION100
2.537-2.73280.15881430.13236934X-RAY DIFFRACTION100
2.7328-3.00780.16831430.13776952X-RAY DIFFRACTION100
3.0078-3.44290.19641430.13946971X-RAY DIFFRACTION100
3.4429-4.33730.15471420.12256938X-RAY DIFFRACTION100
4.3373-47.73710.15871460.13337062X-RAY DIFFRACTION100
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)
11.92490.3423-0.11822.0929-1.02691.48570.0306-0.06150.14840.0293-0.01620.2245-0.2547-0.3376-0.0010.18850.0762-0.0450.2206-0.0430.191924.154112.00123.2108
21.8844-0.4284-0.31070.70570.25411.06860.01820.0279-0.042-0.1522-0.0331-0.0188-0.0337-0.00620.01730.18660.0082-0.0130.1209-0.0090.155444.63510.6666-2.1702
31.1904-0.27970.12610.6547-0.05170.87010.04810.1514-0.0941-0.1904-0.06930.06270.0187-0.09920.01820.20620.0085-0.0250.1664-0.03730.169138.7480.1615-8.0788
42.0601-0.1543-0.37675.0812-3.23143.59750.0709-0.1430.00750.13230.07130.5483-0.2439-0.6769-0.19040.16670.0543-0.05140.4461-0.06270.319513.88247.23333.9131
55.5802-0.3244-3.90261.72550.35722.73650.04430.0369-0.0595-0.04540.20430.37-0.0738-0.3691-0.10840.18810.0145-0.02590.7266-0.02550.53233.24573.172212.1731
65.11862.5696-2.9512.0256-1.38211.71620.5602-0.51730.96240.5727-0.79450.3469-0.02280.1809-0.17820.3974-0.14910.13240.9094-0.02830.6426-32.10615.818132.505
71.7890.2450.56241.5896-0.16491.8375-0.0147-0.1486-0.02160.1378-0.00980.1417-0.0769-0.31680.01980.18680.03340.030.2238-0.01790.152530.30289.095431.7615
81.0873-0.209-0.43730.60590.17491.1578-0.003-0.07770.10070.00330.001-0.0619-0.28760.0404-0.01090.2335-0.0095-0.01830.1207-0.00950.161948.007417.418220.3363
91.4935-0.4735-0.20891.45820.13914.7429-0.0204-0.1993-0.08710.07840.05370.3271-0.0955-0.76860.02110.21770.08750.03080.4027-0.00010.283519.832413.270130.3173
106.70312.1085-1.38160.9853-0.18470.42540.1361-0.8091-0.51890.17270.07110.13080.1962-0.27240.02560.3718-0.0086-0.0181.01390.40320.651-14.83682.022431.2962
110.944-0.4624-0.19931.72580.1861.1548-0.05630.0278-0.11980.0271-0.03920.32240.1644-0.38760.0920.196-0.07770.00920.2589-0.01860.260225.9195-14.86715.3124
120.8747-0.1351-0.08730.5138-0.03060.87170.0109-0.0617-0.0470.0369-0.03080.02310.1321-0.01770.02220.1795-0.02210.00250.12720.0150.158645.4299-11.866820.9899
131.7788-0.3727-0.58831.41520.37291.7254-0.0037-0.0303-0.0217-0.036-0.0236-0.08290.13040.1130.02350.1765-0.0022-0.00940.18850.04130.173260.3261-8.558217.7324
141.42031.097-0.85642.01471.07513.0993-0.0346-0.2296-0.41330.1418-0.0091-0.26250.19920.48660.04630.19670.0248-0.00160.21920.08310.239463.7763-14.503524.1872
150.83320.0516-00.8436-0.00691.0605-0.0179-0.0924-0.16670.1079-0.02950.07370.276-0.09170.02980.2162-0.03210.02410.14650.02270.162941.3314-17.348825.2166
161.2571.49830.94232.28040.41221.7694-0.0976-0.078-0.0086-0.0337-0.02240.57780.0676-0.6060.08760.1882-0.10490.07120.4215-0.02390.356817.2193-13.33522.4661
176.0939-2.47721.1221.7008-0.43330.2080.04090.2206-0.1063-0.0273-0.11430.68550.0483-0.6-0.02370.2787-0.04120.05330.77230.00850.63336.0278-6.398825.5104
187.228-2.6281-3.36825.92281.36316.27970.20740.8001-0.6712-0.0364-0.52480.1210.299-0.16020.32790.3878-0.0499-0.03160.56750.18230.6499-32.2316-1.168425.1018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 169 )
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 266 )
4X-RAY DIFFRACTION4chain 'A' and (resid 267 through 290 )
5X-RAY DIFFRACTION5chain 'A' and (resid 291 through 306 )
6X-RAY DIFFRACTION6chain 'A' and (resid 307 through 337 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 56 )
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 266 )
9X-RAY DIFFRACTION9chain 'B' and (resid 267 through 290 )
10X-RAY DIFFRACTION10chain 'B' and (resid 291 through 335 )
11X-RAY DIFFRACTION11chain 'C' and (resid 17 through 56 )
12X-RAY DIFFRACTION12chain 'C' and (resid 57 through 140 )
13X-RAY DIFFRACTION13chain 'C' and (resid 141 through 169 )
14X-RAY DIFFRACTION14chain 'C' and (resid 170 through 188 )
15X-RAY DIFFRACTION15chain 'C' and (resid 189 through 266 )
16X-RAY DIFFRACTION16chain 'C' and (resid 267 through 290 )
17X-RAY DIFFRACTION17chain 'C' and (resid 291 through 306 )
18X-RAY DIFFRACTION18chain 'C' and (resid 307 through 335 )

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