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- PDB-5eoc: Crystal structure of Fab C2 in complex with a Cyclic variant of H... -

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Basic information

Entry
Database: PDB / ID: 5eoc
TitleCrystal structure of Fab C2 in complex with a Cyclic variant of Hepatitis C Virus E2 epitope I
Components
  • (Fab fragment (Heavy chain)) x 2
  • ALA-CYS-GLN-LEU-ILE-ASN-THR-ASN-GLY-SER-TRP-HIS-ILE-CYS
  • Fab fragment (Light chain)
KeywordsIMMUNE SYSTEM / Complex / monoclonal antibodies / HCV
Function / homology
Function and homology information


positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / SH3 domain binding / kinase binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / 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 NS4b ...Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / 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 NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / 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 protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / 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 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Hepatitis C virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBerisio, R. / Ruggiero, A. / Sandomenico, A. / Patel, A.H. / Ruvo, M. / Vitagliano, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministry of Education, Universities and ResearchRBNE08NKH7_003 Italy
CitationJournal: J.Virol. / Year: 2016
Title: Generation and Characterization of Monoclonal Antibodies against a Cyclic Variant of Hepatitis C Virus E2 Epitope 412-422.
Authors: Sandomenico, A. / Leonardi, A. / Berisio, R. / Sanguigno, L. / Foca, G. / Foca, A. / Ruggiero, A. / Doti, N. / Muscariello, L. / Barone, D. / Farina, C. / Owsianka, A. / Vitagliano, L. / Patel, A.H. / Ruvo, M.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab fragment (Heavy chain)
L: Fab fragment (Light chain)
J: Fab fragment (Heavy chain)
M: Fab fragment (Light chain)
P: ALA-CYS-GLN-LEU-ILE-ASN-THR-ASN-GLY-SER-TRP-HIS-ILE-CYS
Q: ALA-CYS-GLN-LEU-ILE-ASN-THR-ASN-GLY-SER-TRP-HIS-ILE-CYS


Theoretical massNumber of molelcules
Total (without water)97,5426
Polymers97,5426
Non-polymers00
Water8,575476
1
H: Fab fragment (Heavy chain)
L: Fab fragment (Light chain)
P: ALA-CYS-GLN-LEU-ILE-ASN-THR-ASN-GLY-SER-TRP-HIS-ILE-CYS


Theoretical massNumber of molelcules
Total (without water)48,7623
Polymers48,7623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-28 kcal/mol
Surface area19270 Å2
MethodPISA
2
J: Fab fragment (Heavy chain)
M: Fab fragment (Light chain)
Q: ALA-CYS-GLN-LEU-ILE-ASN-THR-ASN-GLY-SER-TRP-HIS-ILE-CYS


Theoretical massNumber of molelcules
Total (without water)48,7793
Polymers48,7793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-28 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.972, 56.191, 77.153
Angle α, β, γ (deg.)90.35, 90.18, 94.98
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Fab fragment (Heavy chain)


Mass: 23395.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab fragment (Light chain)


Mass: 23806.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Fab fragment (Heavy chain)


Mass: 23412.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Protein/peptide ALA-CYS-GLN-LEU-ILE-ASN-THR-ASN-GLY-SER-TRP-HIS-ILE-CYS


Mass: 1560.776 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: P27958*PLUS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulphate and 25% (w/v) PEG 3,350 / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→25 Å / Num. obs: 59746 / % possible obs: 93 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.9
Reflection shellResolution: 1.98→2.05 Å / % possible all: 81.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y5T AND 2Y6S

2y5t

2y6s


Resolution: 1.98→15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.46 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.197
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26565 3000 5.1 %RANDOM
Rwork0.2343 ---
obs-56256 92.35 %-
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 mean: 28.907 Å2
Refinement stepCycle: LAST / Resolution: 1.98→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6732 0 0 476 7208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226914
X-RAY DIFFRACTIONr_bond_other_d0.0010.024593
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9489428
X-RAY DIFFRACTIONr_angle_other_deg0.946311241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7895876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73223.933267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.376151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6621533
X-RAY DIFFRACTIONr_chiral_restr0.0850.21063
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021354
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8791.54398
X-RAY DIFFRACTIONr_mcbond_other0.1641.51770
X-RAY DIFFRACTIONr_mcangle_it1.58727134
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.04132516
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2534.52293
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.977→2.028 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 188 -
Rwork0.319 3528 -
obs--79.74 %

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