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- PDB-2vgq: Crystal Structure of Human IPS-1 CARD -

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Basic information

Entry
Database: PDB / ID: 2vgq
TitleCrystal Structure of Human IPS-1 CARD
ComponentsSugar ABC transporter substrate-binding protein,Mitochondrial antiviral-signaling protein
KeywordsIMMUNE SYSTEM/TRANSPORT / IPS1/MAVS/VISA/CARDIF / CASPASE ACTIVATION / CASPASE RECRUITMENT DOMAIN / INNATE IMMUNITY / FUSION PROTEIN / SUGAR TRANSPORT / TRANSPORT / IMMUNE SYSTEM / CHIMERA / IMMUNE SYSTEM-TRANSPORT complex
Function / homology
Function and homology information


positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / peroxisomal membrane / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of viral genome replication / detection of maltose stimulus / cellular response to exogenous dsRNA / maltose binding / type I interferon-mediated signaling pathway / maltose transport complex / cytoplasmic pattern recognition receptor signaling pathway / maltose transport / maltodextrin transmembrane transport / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / positive regulation of type I interferon production / ubiquitin ligase complex / signaling adaptor activity / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / activation of innate immune response / molecular condensate scaffold activity / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-8 production / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / Ovarian tumor domain proteases / positive regulation of tumor necrosis factor production / outer membrane-bounded periplasmic space / TRAF3-dependent IRF activation pathway / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / periplasmic space / molecular adaptor activity / defense response to bacterium / positive regulation of protein phosphorylation / innate immune response / DNA damage response / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / membrane / identical protein binding
Similarity search - Function
IPS1, CARD domain / Death Domain, Fas / Caspase recruitment domain / Caspase recruitment domain / Death Domain, Fas / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein ...IPS1, CARD domain / Death Domain, Fas / Caspase recruitment domain / Caspase recruitment domain / Death Domain, Fas / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Death-like domain superfamily / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltotetraose / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein / Mitochondrial antiviral-signaling protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPotter, J.A. / Randall, R.E. / Taylor, G.L.
CitationJournal: BMC Struct Biol / Year: 2008
Title: Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain.
Authors: Jane A Potter / Richard E Randall / Garry L Taylor /
Abstract: BACKGROUND: IPS-1/MAVS/VISA/Cardif is an adaptor protein that plays a crucial role in the induction of interferons in response to viral infection. In the initial stage of the intracellular antiviral ...BACKGROUND: IPS-1/MAVS/VISA/Cardif is an adaptor protein that plays a crucial role in the induction of interferons in response to viral infection. In the initial stage of the intracellular antiviral response two RNA helicases, retinoic acid inducible gene-I (RIG-I) and melanoma differentiation-association gene 5 (MDA5), are independently able to bind viral RNA in the cytoplasm. The 62 kDa protein IPS-1/MAVS/VISA/Cardif contains an N-terminal caspase activation and recruitment (CARD) domain that associates with the CARD regions of RIG-I and MDA5, ultimately leading to the induction of type I interferons. As a first step towards understanding the molecular basis of this important adaptor protein we have undertaken structural studies of the IPS-1 MAVS/VISA/Cardif CARD region.
RESULTS: The crystal structure of human IPS-1/MAVS/VISA/Cardif CARD has been determined to 2.1A resolution. The protein was expressed and crystallized as a maltose-binding protein (MBP) fusion ...RESULTS: The crystal structure of human IPS-1/MAVS/VISA/Cardif CARD has been determined to 2.1A resolution. The protein was expressed and crystallized as a maltose-binding protein (MBP) fusion protein. The MBP and IPS-1 components each form a distinct domain within the structure. IPS-1/MAVS/VISA/Cardif CARD adopts a characteristic six-helix bundle with a Greek-key topology and, in common with a number of other known CARD structures, contains two major polar surfaces on opposite sides of the molecule. One face has a surface-exposed, disordered tryptophan residue that may explain the poor solubility of untagged expression constructs.
CONCLUSION: The IPS-1/MAVS/VISA/Cardif CARD domain adopts the classic CARD fold with an asymmetric surface charge distribution that is typical of CARD domains involved in homotypic protein-protein ...CONCLUSION: The IPS-1/MAVS/VISA/Cardif CARD domain adopts the classic CARD fold with an asymmetric surface charge distribution that is typical of CARD domains involved in homotypic protein-protein interactions. The location of the two polar areas on IPS-1/MAVS/VISA/Cardif CARD suggest possible types of associations that this domain makes with the two CARD domains of MDA5 or RIG-I. The N-terminal CARD domains of RIG-I and MDA5 share greatest sequence similarity with IPS-1/MAVS/VISA/Cardif CARD and this has allowed modelling of their structures. These models show a very different charge profile for the equivalent surfaces compared to IPS-1/MAVS/VISA/Cardif CARD.
History
DepositionNov 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar ABC transporter substrate-binding protein,Mitochondrial antiviral-signaling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5587
Polymers53,4111
Non-polymers1,1476
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.260, 99.260, 163.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Sugar ABC transporter substrate-binding protein,Mitochondrial antiviral-signaling protein / MAVS / CARD adapter inducing interferon beta / Cardif / Interferon beta promoter stimulator protein ...MAVS / CARD adapter inducing interferon beta / Cardif / Interferon beta promoter stimulator protein 1 / IPS-1 / Putative NF-kappa-B-activating protein 031N / Virus-induced-signaling adapter / VISA


Mass: 53411.324 Da / Num. of mol.: 1
Fragment: MMBP RESIDUES 27-392, CARD DOMAIN RESIDUES 3-93,MMBP RESIDUES 27-392, CARD DOMAIN RESIDUES 3-93
Source method: isolated from a genetically manipulated source
Details: THE CONSTRUCT IS A FUSION OF E. COLI MBP (RESIDUES 2-366) AND HUMAN IPS-1 CARD (RESIDUES 1 TO 93)
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, PU06_05845, MAVS, IPS1, KIAA1271, VISA / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: A0A0B1N7A9, UniProt: Q7Z434, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→32.7 Å / Num. obs: 48262 / % possible obs: 99.8 % / Observed criterion σ(I): 4.4 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.24 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.449 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2404 5 %RANDOM
Rwork0.181 ---
obs0.183 45853 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 70 203 3885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9775229
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5595477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05825.257175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03315629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2621514
X-RAY DIFFRACTIONr_chiral_restr0.1050.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022904
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21763
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22632
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8681.52399
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33223741
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32431677
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.434.51479
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 162
Rwork0.222 3349

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