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- PDB-2rhk: Crystal structure of influenza A NS1A protein in complex with F2F... -

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Basic information

Entry
Database: PDB / ID: 2rhk
TitleCrystal structure of influenza A NS1A protein in complex with F2F3 fragment of human cellular factor CPSF30, Northeast Structural Genomics Targets OR8C and HR6309A
Components
  • Cleavage and polyadenylation specificity factor subunit 4
  • Non-structural protein 1
KeywordsVIRAL PROTEIN/NUCLEAR PROTEIN / Influenza A / Nonstructural protein / viral protein: host complex / Zn finger / Alternative splicing / Cytoplasm / Host-virus interaction / Interferon antiviral system evasion / Nucleus / RNA-binding / Suppressor of RNA silencing / Metal-binding / mRNA processing / Zinc / Zinc-finger / METAL BINDING PROTEIN / VIRAL PROTEIN-METAL BINDING PROTEIN COMPLEX / VIRAL PROTEIN-NUCLEAR PROTEIN COMPLEX / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


symbiont-mediated perturbation of host intracellular transport / symbiont-mediated suppression of host innate immune response / : / Inhibition of Host mRNA Processing and RNA Silencing / suppression by virus of host cytokine production / symbiont-mediated suppression of host mRNA processing / Processing of Intronless Pre-mRNAs / symbiont-mediated suppression of host PKR/eIFalpha signaling / mRNA cleavage and polyadenylation specificity factor complex / protein serine/threonine kinase inhibitor activity ...symbiont-mediated perturbation of host intracellular transport / symbiont-mediated suppression of host innate immune response / : / Inhibition of Host mRNA Processing and RNA Silencing / suppression by virus of host cytokine production / symbiont-mediated suppression of host mRNA processing / Processing of Intronless Pre-mRNAs / symbiont-mediated suppression of host PKR/eIFalpha signaling / mRNA cleavage and polyadenylation specificity factor complex / protein serine/threonine kinase inhibitor activity / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / tRNA processing in the nucleus / RNA Polymerase II Transcription Termination / Processing of Capped Intron-Containing Pre-mRNA / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / mRNA processing / sequence-specific double-stranded DNA binding / double-stranded RNA binding / host cell cytoplasm / intracellular membrane-bounded organelle / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / RNA binding / zinc ion binding / nucleoplasm / identical protein binding
Similarity search - Function
Zinc finger, CCCH-type / CCCH zinc finger / Zinc-finger CCCH domain / Zinc-finger containing family / CPSF complex subunit CPSF4-like / Influenza virus non-structural protein, effector domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) ...Zinc finger, CCCH-type / CCCH zinc finger / Zinc-finger CCCH domain / Zinc-finger containing family / CPSF complex subunit CPSF4-like / Influenza virus non-structural protein, effector domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Few Secondary Structures / Irregular / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / S15/NS1, RNA-binding / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Cleavage and polyadenylation specificity factor subunit 4 / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A Virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsDas, K. / Ma, L.-C. / Xiao, R. / Radvansky, B. / Aramini, J. / Zhao, L. / Arnold, E. / Krug, R.M. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural basis for suppression of a host antiviral response by influenza A virus.
Authors: Das, K. / Ma, L.C. / Xiao, R. / Radvansky, B. / Aramini, J. / Zhao, L. / Marklund, J. / Kuo, R.L. / Twu, K.Y. / Arnold, E. / Krug, R.M. / Montelione, G.T.
History
DepositionOct 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1
C: Cleavage and polyadenylation specificity factor subunit 4
D: Cleavage and polyadenylation specificity factor subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,76414
Polymers49,0704
Non-polymers69410
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
MethodPISA
2
A: Non-structural protein 1
C: Cleavage and polyadenylation specificity factor subunit 4
D: Cleavage and polyadenylation specificity factor subunit 4
hetero molecules

A: Non-structural protein 1
B: Non-structural protein 1
D: Cleavage and polyadenylation specificity factor subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,80023
Polymers73,6066
Non-polymers1,19517
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4870 Å2
MethodPISA
3
A: Non-structural protein 1
C: Cleavage and polyadenylation specificity factor subunit 4
D: Cleavage and polyadenylation specificity factor subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,80013
Polymers33,1063
Non-polymers69410
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
MethodPISA
4
A: Non-structural protein 1
B: Non-structural protein 1
D: Cleavage and polyadenylation specificity factor subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,00110
Polymers40,5003
Non-polymers5017
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.960, 50.960, 205.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 15964.370 Da / Num. of mol.: 2 / Fragment: NS1A effector domain (UNP residues 85-215)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A Virus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03495
#2: Protein Cleavage and polyadenylation specificity factor subunit 4 / / Cleavage and polyadenylation specificity factor 30 kDa subunit / CPSF 30 kDa subunit / NS1 effector ...Cleavage and polyadenylation specificity factor 30 kDa subunit / CPSF 30 kDa subunit / NS1 effector domain-binding protein 1 / Neb-1 / No arches homolog / F2F3 Zinc-binding domains


Mass: 8570.844 Da / Num. of mol.: 2 / Fragment: F2F3 Zinc-binding domains (UNP residues 61-121) / Mutation: P94S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O95639

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Non-polymers , 4 types, 195 molecules

#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 0.5 M KNO3, 10% sucroes, 0.1M sodium acitate, pH 5.5, EVAPORATION, temperature 293K, pH 5.50

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98 / Wavelength: 0.9786, 0.9790, 0.9650
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.97861
30.9791
40.9651
ReflectionResolution: 1.95→50 Å / Num. obs: 37297 / % possible obs: 97.7 % / Observed criterion σ(I): -0.5 / Redundancy: 5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % possible all: 88.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1225055.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1159 3.1 %RANDOM
Rwork0.21 ---
obs0.21 37096 97.8 %-
all-37297 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.03 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-6.66 Å20 Å20 Å2
2--6.66 Å20 Å2
3----13.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-6 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 32 185 3128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 170 2.9 %
Rwork0.27 5620 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4NO3.PARNO3.TOP
X-RAY DIFFRACTION5TRS.PARTRS.TOP

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