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- PDB-7wz5: Larimichthys crocea IFNi -

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Basic information

Entry
Database: PDB / ID: 7wz5
TitleLarimichthys crocea IFNi
ComponentsInterferon C
KeywordsCYTOKINE / interferon / antiviral
Function / homology
Function and homology information


cytokine receptor binding / defense response to virus / extracellular region
Similarity search - Function
Interferon alpha/beta/delta / Interferon alpha/beta domain / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesLarimichthys crocea (large yellow croaker)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsChen, J.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Citation
Journal: J Immunol. / Year: 2024
Title: Structural and Functional Characterization of a Fish Type I Subgroup d IFN Reveals Its Binding to Receptors.
Authors: Guan, Y. / Chen, J. / Guan, H. / Chen, T.T. / Teng, Y. / Wei, Z. / Li, Z. / Ouyang, S. / Chen, X.
#1: Journal: J Immunol. / Year: 2022
Title: Molecular and Structural Basis of Receptor Binding and Signaling of a Fish Type I IFN with Three Disulfide Bonds.
Authors: Chen, J. / Guan, Y. / Guan, H. / Mu, Y. / Ding, Y. / Zou, J. / Ouyang, S. / Chen, X.
History
DepositionFeb 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1962
Polymers17,9751
Non-polymers2211
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint4 kcal/mol
Surface area8760 Å2
Unit cell
Length a, b, c (Å)36.310, 60.620, 81.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Interferon C


Mass: 17975.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Larimichthys crocea (large yellow croaker)
Gene: D5F01_LYC18041 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A3G3BTG1
#2: 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 natural 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 289.15 K / Method: evaporation
Details: Calcium chloride dihydrate, BIS-TRIS, Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979176 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 1.39→34 Å / Num. obs: 36077 / % possible obs: 97.85 % / Redundancy: 5 % / Biso Wilson estimate: 22.47 Å2 / CC1/2: 0.997 / Net I/σ(I): 30.97
Reflection shellResolution: 1.39→1.43 Å / Num. unique obs: 36077 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
xia21data scaling
PDB_EXTRACT1data extraction
xia21data reduction
PARROT1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PIW

3piw


Resolution: 1.39→33.15 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 1817 5.04 %RANDOM
Rwork0.1986 ---
obs0.1993 36077 97.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 14 97 1367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061303
X-RAY DIFFRACTIONf_angle_d0.8291774
X-RAY DIFFRACTIONf_dihedral_angle_d4.839176
X-RAY DIFFRACTIONf_chiral_restr0.073196
X-RAY DIFFRACTIONf_plane_restr0.005230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.430.35111440.32882463X-RAY DIFFRACTION94
1.43-1.470.31581290.2862557X-RAY DIFFRACTION96
1.47-1.520.24791240.23832569X-RAY DIFFRACTION96
1.52-1.570.23211440.20822569X-RAY DIFFRACTION98
1.57-1.630.21641450.19962614X-RAY DIFFRACTION98
1.63-1.710.2121430.21112609X-RAY DIFFRACTION98
1.71-1.80.23711160.21252628X-RAY DIFFRACTION98
1.8-1.910.23091510.2042661X-RAY DIFFRACTION98
1.91-2.060.21521470.19452640X-RAY DIFFRACTION99
2.06-2.270.19121390.18112690X-RAY DIFFRACTION99
2.27-2.590.21311310.18842719X-RAY DIFFRACTION99
2.59-3.270.19681580.19832723X-RAY DIFFRACTION100
3.27-33.150.21161460.19492818X-RAY DIFFRACTION98
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)
15.82641.1959-3.47664.6907-1.35186.78650.13240.15580.1455-0.0319-0.0363-0.2295-0.0570.2829-0.14850.17010.0253-0.01950.1559-0.01660.21325.246619.081454.4647
20.80041.69240.35475.1991-0.99423.1629-0.0545-0.1668-0.07250.52710.0818-0.1330.23160.2368-0.04040.22480.02580.00540.22120.03010.245115.61181.689563.1062
34.8053-3.6820.26284.46091.08521.0338-1.0721-0.9102-1.4217-0.19610.0603-0.30861.43481.19830.69690.46590.14990.19530.39930.09210.435634.98643.486144.3524
43.4628-1.2818-3.65093.46760.28364.5295-0.03150.5978-0.3261-0.2012-0.03940.17690.1805-0.2930.0520.2291-0.0036-0.03240.22410.00920.1717.222410.783647.5671
53.6825-0.2196-1.4371.78880.25934.98580.1619-0.80350.28850.7739-0.28890.94120.1139-0.74310.06750.4203-0.01710.14610.3457-0.01770.37076.263213.994666.3608
62.31650.0105-0.39183.2886-0.03722.4850.05190.11120.59130.0833-0.03850.2688-0.6875-0.485-0.0770.22220.0362-0.02090.21120.01190.280916.126321.710353.5163
74.48142.1975-0.86033.8937-3.39384.6904-0.13870.859-0.7065-1.2602-0.02750.23810.96820.00010.27410.46550.0567-0.04090.4927-0.0770.446818.4767.939240.5359
86.8911-0.3459-0.67034.70890.81966.1166-0.03610.1698-0.32690.2361-0.03890.45070.1661-0.71220.08160.1681-0.0267-0.01740.20050.03960.24226.56262.96456.0893
96.21040.9418-2.35792.8926-1.03323.6682-0.0837-0.3979-0.36180.1667-0.1102-0.04580.10740.26850.18340.19010.0156-0.00280.13540.02170.143119.95688.088459.3228
105.0333-1.4833-0.40262.2022-1.83487.494-0.0604-0.0760.0684-0.3954-0.2703-0.6415-0.19110.3490.30430.190.0058-0.01450.2360.04430.23733.5716.742949.1775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 73 )
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 86 )
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 103 )
7X-RAY DIFFRACTION7chain 'A' and (resid 104 through 116 )
8X-RAY DIFFRACTION8chain 'A' and (resid 117 through 132 )
9X-RAY DIFFRACTION9chain 'A' and (resid 133 through 154 )
10X-RAY DIFFRACTION10chain 'A' and (resid 155 through 162 )

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