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- PDB-1kac: KNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12 IN COMPLEX WITH DOMAIN 1 ... -

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Basic information

Entry
Database: PDB / ID: 1kac
TitleKNOB DOMAIN FROM ADENOVIRUS SEROTYPE 12 IN COMPLEX WITH DOMAIN 1 OF ITS CELLULAR RECEPTOR CAR
Components
  • PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)
  • PROTEIN (FIBER KNOB PROTEIN)
KeywordsViral protein/receptor / ADHESION PROTEIN RECEPTOR COMPLEX / VIRAL PROTEIN-RECEPTOR COMPLEX
Function / homology
Function and homology information


AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / connexin binding ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / connexin binding / transepithelial transport / cell-cell junction organization / adhesion receptor-mediated virion attachment to host cell / cardiac muscle cell development / heterophilic cell-cell adhesion / intercalated disc / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / Cell surface interactions at the vascular wall / mitochondrion organization / adherens junction / PDZ domain binding / filopodium / neuromuscular junction / beta-catenin binding / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / cell junction / viral capsid / heart development / cell body / virus receptor activity / growth cone / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / cell adhesion / neuron projection / membrane raft / signaling receptor binding / symbiont entry into host cell / host cell nucleus / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain ...: / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fiber protein / Coxsackievirus and adenovirus receptor
Similarity search - Component
Biological speciesHuman adenovirus 12
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å
AuthorsBewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M.
CitationJournal: Science / Year: 1999
Title: Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR.
Authors: Bewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M.
History
DepositionMay 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (FIBER KNOB PROTEIN)
B: PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)


Theoretical massNumber of molelcules
Total (without water)33,5852
Polymers33,5852
Non-polymers00
Water1,26170
1
A: PROTEIN (FIBER KNOB PROTEIN)
B: PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)

A: PROTEIN (FIBER KNOB PROTEIN)
B: PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)

A: PROTEIN (FIBER KNOB PROTEIN)
B: PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)


Theoretical massNumber of molelcules
Total (without water)100,7556
Polymers100,7556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
Unit cell
Length a, b, c (Å)167.850, 167.850, 167.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein PROTEIN (FIBER KNOB PROTEIN)


Mass: 19944.477 Da / Num. of mol.: 1 / Fragment: KNOB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 12 / Genus: Mastadenovirus / Species: Human adenovirus A / Variant: SEROTYPE 12 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / Variant (production host): T7 / References: UniProt: P36711
#2: Protein PROTEIN (COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR)


Mass: 13640.500 Da / Num. of mol.: 1 / Fragment: DOMAIN 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P78310
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
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: 5.6 Å3/Da / Density % sol: 78 %
Crystal growpH: 6.2 / Details: 900MM AMMONIUM SULPHATE ON 100MM MES, PH 6.2
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.9 Mammonium sulfate1reservoir
2100 mMMES1reservoirpH6.2

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 24636 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.7
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.35 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
AMoREphasing
CNS5refinement
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.6→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 739 2.9 %RANDOM
Rwork0.22 ---
obs0.22 24601 96.8 %-
Solvent computationBsol: 61 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 0 70 2430
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM
Software
*PLUS
Name: CNS / Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 2.9 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.9 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.7

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