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- PDB-1fpt: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN THE FAB FRAGME... -

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Basic information

Entry
Database: PDB / ID: 1fpt
TitleTHREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN THE FAB FRAGMENT OF AN NEUTRALIZING ANTIBODY FOR TYPE 1 POLIOVIRUS AND ITS VIRAL EPITOPE
Components
  • FAB FRAGMENT OF AN NEUTRALIZING ANTIBODY FOR TYPE 1 POLIOVIRUS
  • IGG2A-KAPPA C3 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA C3 FAB (LIGHT CHAIN)
KeywordsCOMPLEX (ANTIBODY/PV-1 FRAGMENT) / COMPLEX (ANTIBODY-PV-1 FRAGMENT) / COMPLEX (ANTIBODY-PV-1 FRAGMENT) complex
Function / homology
Function and homology information


positive regulation of B cell activation / symbiont-mediated suppression of host translation initiation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment ...positive regulation of B cell activation / symbiont-mediated suppression of host translation initiation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport / antigen processing and presentation / immunoglobulin mediated immune response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / regulation of proteolysis / positive regulation of endocytosis / complement activation, classical pathway / antigen binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / multivesicular body / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / positive regulation of phagocytosis / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / response to bacterium / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / positive regulation of immune response / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...: / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 2A / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsWien, M.W. / Hogle, J.M.
CitationJournal: Nat.Struct.Biol. / Year: 1995
Title: Structure of the complex between the Fab fragment of a neutralizing antibody for type 1 poliovirus and its viral epitope.
Authors: Wien, M.W. / Filman, D.J. / Stura, E.A. / Guillot, S. / Delpeyroux, F. / Crainic, R. / Hogle, J.M.
History
DepositionJan 26, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 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
P: FAB FRAGMENT OF AN NEUTRALIZING ANTIBODY FOR TYPE 1 POLIOVIRUS
L: IGG2A-KAPPA C3 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA C3 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)49,4993
Polymers49,4993
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.785, 129.785, 143.829
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141
4: ARG H 40 - PRO H 41 OMEGA = 247.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: CIS PROLINE - PRO H 149 / 6: CIS PROLINE - PRO H 151

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Components

#1: Antibody FAB FRAGMENT OF AN NEUTRALIZING ANTIBODY FOR TYPE 1 POLIOVIRUS


Mass: 1940.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03299, UniProt: P03300*PLUS
#2: Antibody IGG2A-KAPPA C3 FAB (LIGHT CHAIN)


Mass: 24080.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#3: Antibody IGG2A-KAPPA C3 FAB (HEAVY CHAIN)


Mass: 23478.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01865
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FAB FRAGMENT IS NUMBERED ACCORDING TO THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, M. REID- ...THE FAB FRAGMENT IS NUMBERED ACCORDING TO THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, M. REID-MILLER, H.M. PERRY, K.S. GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 4TH ED., (1987), NATIONAL INSTITUTE OF HEALTH, BETHESDA, MD. THE PEPTIDE IS NUMBERED ACCORDING TO THE POLIOVIRUS TYPE 1 SEQUENCE (MAHONEY STRAIN) (V.R. RANCANIELLO AND D. BALTIMORE (1981) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, USA V. 78, 4887-4891). THE PEPTIDE USED WAS A SYNTHETIC HOMOLOGUE OF RESIDUES 86 - 103 OF PV-1 VP1 (MAHONEY STRAIN). PV-1 VP1 RESIDUES ARE (CVTIMYVDNPASTTNKDK). DUE TO DISORDER, RESIDUES 86 - 92 ARE NOT PRESENTED IN THE RECORDS BELOW.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlFab1drop
210 mg/mlpeptide1drop
31.1 MNa citrate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 13342 / % possible obs: 86 % / Observed criterion σ(I): 15.6 / Num. measured all: 87269 / Rmerge(I) obs: 0.0986

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.23 -
obs0.23 13342
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 0 39 3465
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2

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