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- PDB-1qgc: STRUCTURE OF THE COMPLEX OF A FAB FRAGMENT OF A NEUTRALIZING ANTI... -

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Entry
Database: PDB / ID: 1qgc
TitleSTRUCTURE OF THE COMPLEX OF A FAB FRAGMENT OF A NEUTRALIZING ANTIBODY WITH FOOT AND MOUTH DISEASE VIRUS
Components
  • (PROTEIN (IMMUNOGLOBULIN ...) x 2
  • (PROTEIN (VIRUS CAPSID PROTEIN ...) x 3
  • PROTEIN (GH-LOOP FROM VIRUS CAPSID PROTEIN VP1)
KeywordsVirus/Immune system / VIRUS-ANTIBODY COMPLEX / Icosahedral virus / Virus-Immune system COMPLEX
Function / homology
Function and homology information


: / L-peptidase / modulation by virus of host chromatin organization / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / IgG immunoglobulin complex / picornain 3C / ribonucleoside triphosphate phosphatase activity / B cell differentiation ...: / L-peptidase / modulation by virus of host chromatin organization / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / IgG immunoglobulin complex / picornain 3C / ribonucleoside triphosphate phosphatase activity / B cell differentiation / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / regulation of translation / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / extracellular region / ATP binding / membrane / plasma membrane
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Papain-like cysteine peptidase superfamily / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Immunoglobulin kappa constant / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus - type C
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 30 Å
AuthorsFita, I.
CitationJournal: EMBO J / Year: 1997
Title: Structure of the complex of an Fab fragment of a neutralizing antibody with foot-and-mouth disease virus: positioning of a highly mobile antigenic loop.
Authors: E A Hewat / N Verdaguer / I Fita / W Blakemore / S Brookes / A King / J Newman / E Domingo / M G Mateu / D I Stuart /
Abstract: Data from cryo-electron microscopy and X-ray crystallography have been combined to study the interactions of foot-and-mouth disease virus serotype C (FMDV-C) with a strongly neutralizing monoclonal ...Data from cryo-electron microscopy and X-ray crystallography have been combined to study the interactions of foot-and-mouth disease virus serotype C (FMDV-C) with a strongly neutralizing monoclonal antibody (mAb) SD6. The mAb SD6 binds to the long flexible GH-loop of viral protein 1 (VP1) which also binds to an integrin receptor. The structure of the virus-Fab complex was determined to 30 A resolution using cryo-electron microscopy and image analysis. The known structure of FMDV-C, and of the SD6 Fab co-crystallized with a synthetic peptide corresponding to the GH-loop of VP1, were fitted to the cryo-electron microscope density map. The SD6 Fab is seen to project almost radially from the viral surface in an orientation which is only compatible with monovalent binding of the mAb. Even taking into account the mAb hinge and elbow flexibility, it is not possible to model bivalent binding without severely distorting the Fabs. The bound GH-loop is essentially in what has previously been termed the 'up' position in the best fit Fab orientation. The SD6 Fab interacts almost exclusively with the GH-loop of VP1, making very few other contacts with the viral capsid. The position and orientation of the SD6 Fab bound to FMDV-C is in accord with previous immunogenic data.
History
DepositionApr 23, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 19, 2011Group: Atomic model
Revision 1.4Jan 14, 2015Group: Structure summary
Revision 1.5Jul 18, 2018Group: Data collection / Database references / Category: em_image_scans / em_software / struct_ref_seq
Item: _em_software.image_processing_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.6Apr 10, 2019Group: Data collection / Database references / Derived calculations
Category: struct_conn / struct_ref
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_name
Revision 1.7Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
1: PROTEIN (VIRUS CAPSID PROTEIN VP1)
2: PROTEIN (VIRUS CAPSID PROTEIN VP2)
3: PROTEIN (VIRUS CAPSID PROTEIN VP3)
4: PROTEIN (IMMUNOGLOBULIN LIGHT CHAIN)
A: PROTEIN (IMMUNOGLOBULIN HEAVY CHAIN)
5: PROTEIN (GH-LOOP FROM VIRUS CAPSID PROTEIN VP1)


Theoretical massNumber of molelcules
Total (without water)120,9056
Polymers120,9056
Non-polymers00
Water0
1
1: PROTEIN (VIRUS CAPSID PROTEIN VP1)
2: PROTEIN (VIRUS CAPSID PROTEIN VP2)
3: PROTEIN (VIRUS CAPSID PROTEIN VP3)
4: PROTEIN (IMMUNOGLOBULIN LIGHT CHAIN)
A: PROTEIN (IMMUNOGLOBULIN HEAVY CHAIN)
5: PROTEIN (GH-LOOP FROM VIRUS CAPSID PROTEIN VP1)
x 60


Theoretical massNumber of molelcules
Total (without water)7,254,326360
Polymers7,254,326360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: PROTEIN (VIRUS CAPSID PROTEIN VP1)
2: PROTEIN (VIRUS CAPSID PROTEIN VP2)
3: PROTEIN (VIRUS CAPSID PROTEIN VP3)
4: PROTEIN (IMMUNOGLOBULIN LIGHT CHAIN)
A: PROTEIN (IMMUNOGLOBULIN HEAVY CHAIN)
5: PROTEIN (GH-LOOP FROM VIRUS CAPSID PROTEIN VP1)
x 5


  • icosahedral pentamer
  • 605 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)604,52730
Polymers604,52730
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: PROTEIN (VIRUS CAPSID PROTEIN VP1)
2: PROTEIN (VIRUS CAPSID PROTEIN VP2)
3: PROTEIN (VIRUS CAPSID PROTEIN VP3)
4: PROTEIN (IMMUNOGLOBULIN LIGHT CHAIN)
A: PROTEIN (IMMUNOGLOBULIN HEAVY CHAIN)
5: PROTEIN (GH-LOOP FROM VIRUS CAPSID PROTEIN VP1)
x 6


  • icosahedral 23 hexamer
  • 725 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)725,43336
Polymers725,43336
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

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PROTEIN (VIRUS CAPSID PROTEIN ... , 3 types, 3 molecules 123

#1: Protein PROTEIN (VIRUS CAPSID PROTEIN VP1)


Mass: 22667.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type C / Genus: Aphthovirus / Species: Foot-and-mouth disease virus / Strain: SEROTYPE C / References: UniProt: Q9QCE2, UniProt: P03311*PLUS
#2: Protein PROTEIN (VIRUS CAPSID PROTEIN VP2)


Mass: 24297.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type C / Genus: Aphthovirus / Species: Foot-and-mouth disease virus / Strain: SEROTYPE C / References: UniProt: Q9QCE2, UniProt: P03311*PLUS
#3: Protein PROTEIN (VIRUS CAPSID PROTEIN VP3)


Mass: 24020.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type C / Genus: Aphthovirus / Species: Foot-and-mouth disease virus / Strain: SEROTYPE C / References: UniProt: P15072, UniProt: P03311*PLUS

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Protein/peptide , 1 types, 1 molecules 5

#6: Protein/peptide PROTEIN (GH-LOOP FROM VIRUS CAPSID PROTEIN VP1)


Mass: 2463.722 Da / Num. of mol.: 1 / Fragment: RESIDUES 133-156 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type C / Genus: Aphthovirus / Species: Foot-and-mouth disease virus / Strain: SEROTYPE C / References: UniProt: P03311*PLUS

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Antibody , 2 types, 2 molecules 4A

#4: Antibody PROTEIN (IMMUNOGLOBULIN LIGHT CHAIN)


Mass: 24013.379 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#5: Antibody PROTEIN (IMMUNOGLOBULIN HEAVY CHAIN)


Mass: 23442.508 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FAB FRAGMENT OF A NEUTRALIZING ANTIBODY WITH FOOT AND MOUTH DISEASE VIRUS
Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportFilm material: HOLEY CARBON / Grid mesh size: 400 divisions/in.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.5-11.5 %satammonium sulfate1reservoir
210 mMdithiothreitol1reservoir

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Electron microscopy imaging

MicroscopyModel: JEOL 2000EXII
Electron gunAccelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 30000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategoryDetails
1GAPmodel fitting
2X-PLORmodel fitting
3MRC3D reconstructionMRC AND CTF CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionSymmetry type: POINT
Atomic model buildingSpace: REAL
Details: DETAILS--THE ATOMIC MODEL WAS GENERATED USING THE 3D MAP DETERMINED BY CRYO-ELECTRON MICROSCOPY. X-RAY ATOMIC STRUCTURES WERE AVAILABLE FOR THE INTACT PARTICLE OF FMDV-C AND THE SD6 FAB CO- ...Details: DETAILS--THE ATOMIC MODEL WAS GENERATED USING THE 3D MAP DETERMINED BY CRYO-ELECTRON MICROSCOPY. X-RAY ATOMIC STRUCTURES WERE AVAILABLE FOR THE INTACT PARTICLE OF FMDV-C AND THE SD6 FAB CO-CRYSTALLIZED WITH A SYNTHETIC PEPTIDE CORRESPONDING TO THE DOMINANT ANTIGENIC LOOP, THE GH LOOP, FROM THE VIRAL CAPSIDE PROTEIN VP1. THE ATOMIC MODEL WAS OBTAINED BY DOCKING THE TWO CRYSTALLOGRAPHIC STRUCTURES IN THE RECONSTRUCTED EM MAP. FITTING WAS DONE SIMULTANEOUSLY IN REAL AND RECIPROCAL SPACE. IN REAL SPACE THE CALCULATED ELECTRON DENSITY FOR THE STARTING MODELS WERE FITTED INTO THE CRYO-EM DENSITY BY A STEEPEST DESCENT PROCEDURE WHICH OPTIMIZED THE LINEAR CORRELATION COEFFICIENT BETWEEN THE TWO DISTRIBUTION (GAP- J.GRIMES,D.STUART, UNPUBLISHED) FOR THE RECIPROCAL SPACE FITTING THE STRUCTURE FACTORS CORRESPONDING TO THE CRYO-EM DENSITY OF THE COMPLEX WERE CALCULATED BY INVERSE FOURIER TRANSFORMATIONS AND THESE FACTORS AND PHASES WERE USED TO REFINE THE X-RAY STRUCTURES, BY RIGID BODY MINIMIZATION, USING X-PLOR (BRUNGER, ET.AL., 1993, YALE UNIVERSITY)
Atomic model buildingPDB-ID: 1FMD

1fmd


Accession code: 1FMD / Source name: PDB / Type: experimental model
RefinementHighest resolution: 30 Å
Refinement stepCycle: LAST / Highest resolution: 30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8279 0 0 0 8279

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