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- EMDB-45726: Cryo-EM model derived from localized reconstruction of human aden... -

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Entry
Database: EMDB / ID: EMD-45726
TitleCryo-EM model derived from localized reconstruction of human adenovirus 5 (Ad5)-hexon-FII complex at 3.9A resolution
Map data
Sample
  • Complex: Human adenovirus 5 (Ad5) in complex with Coagulation factor FII
    • Organelle or cellular component: Hexon protein
      • Organelle or cellular component: Human Coagulation Factor II
        • Protein or peptide: Prothrombin
      • Protein or peptide: Hexon protein
  • Ligand: CALCIUM ION
KeywordsAdenovirus / Hexon / Coagulation factor X / Coagulation factor II / Prothrombin / Complex / Interactions / VIRUS
Function / homology
Function and homology information


T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation ...T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / negative regulation of proteolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / Regulation of Complement cascade / acute-phase response / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / lipopolysaccharide binding / growth factor activity / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / response to wounding / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / viral capsid / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / host cell / positive regulation of protein phosphorylation / positive regulation of cell growth / : / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / symbiont entry into host cell / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / host cell nucleus / structural molecule activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Group II dsDNA virus coat/capsid protein / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily ...Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Group II dsDNA virus coat/capsid protein / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Prothrombin / Hexon protein
Similarity search - Component
Biological speciesHuman adenovirus 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.13 Å
AuthorsReddy VS / Ma OX
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161367 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structure-derived insights from blood factors binding to the surfaces of different adenoviruses.
Authors: Haley E Mudrick / Shao-Chia Lu / Janarjan Bhandari / Mary E Barry / Jack R Hemsath / Felix G M Andres / Olivia X Ma / Michael A Barry / Vijay S Reddy /
Abstract: The tropism of adenoviruses (Ads) is significantly influenced by the binding of various blood factors. To investigate differences in their binding, we conducted cryo-EM analysis on complexes of ...The tropism of adenoviruses (Ads) is significantly influenced by the binding of various blood factors. To investigate differences in their binding, we conducted cryo-EM analysis on complexes of several human adenoviruses with human platelet factor-4 (PF4), coagulation factors FII (Prothrombin), and FX. While we observed EM densities for FII and FX bound to all the species-C adenoviruses examined, no densities were seen for PF4, even though PF4 can co-pellet with various Ads. Similar to FX, the γ-carboxyglutamic acid (Gla) domain of FII binds within the surface cavity of hexon trimers. While FII binds equally to species-C Ads: Ad5, Ad6, and Ad657, FX exhibits significantly better binding to Ad5 and Ad657 compared to Ad6. Although only the FX-Gla domain is observed at high-resolution (3.7 Å), the entire FX is visible at low-resolution bound to Ad5 in three equivalent binding modes consistent with the 3-fold symmetric hexon. Only the Gla and kringle-1 domains of FII are visible on all the species-C adenoviruses, where the rigid FII binds in an upright fashion, in contrast to the flexible and bent FX. These data suggest that differential binding of FII and FX may shield certain species-C adenoviruses differently against immune molecules, thereby modulating their tropism.
History
DepositionJul 11, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45726.png

Downloads & links

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Map

FileDownload / File: emd_45726.map.gz / Format: CCP4 / Size: 4.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
1.41 Å/pix.
x 92 pix.
= 211.2 Å		1.41 Å/pix.
x 79 pix.
= 129.536 Å		1.41 Å/pix.
x 150 pix.
= 111.232 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.408 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.06616439 - 0.11263617
Average (Standard dev.)0.0018301925 (±0.011044354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-39-48-50
Dimensions7915092
Spacing9215079
CellA: 129.536 Å / B: 211.2 Å / C: 111.232 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45726_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45726_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human adenovirus 5 (Ad5) in complex with Coagulation factor FII

EntireName: Human adenovirus 5 (Ad5) in complex with Coagulation factor FII
Components
  • Complex: Human adenovirus 5 (Ad5) in complex with Coagulation factor FII
    • Organelle or cellular component: Hexon protein
      • Organelle or cellular component: Human Coagulation Factor II
        • Protein or peptide: Prothrombin
      • Protein or peptide: Hexon protein
  • Ligand: CALCIUM ION

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Supramolecule #1: Human adenovirus 5 (Ad5) in complex with Coagulation factor FII

SupramoleculeName: Human adenovirus 5 (Ad5) in complex with Coagulation factor FII
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Cryo-EM model derived from localized reconstruction
Source (natural)Organism: Human adenovirus 5
Molecular weightTheoretical: 400 KDa

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Supramolecule #2: Hexon protein

SupramoleculeName: Hexon protein / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human adenovirus 5

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Supramolecule #3: Human Coagulation Factor II

SupramoleculeName: Human Coagulation Factor II / type: organelle_or_cellular_component / ID: 3 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 5
Molecular weightTheoretical: 108.107617 KDa
SequenceString: MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNPCEWDEAA TALEINLEEE DDDNEDEVDE Q AEQQKTHV ...String:
MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNPCEWDEAA TALEINLEEE DDDNEDEVDE Q AEQQKTHV FGQAPYSGIN ITKEGIQIGV EGQTPKYADK TFQPEPQIGE SQWYETEINH AAGRVLKKTT PMKPCYGSYA KP TNENGGQ GILVKQQNGK LESQVEMQFF STTEATAGNG DNLTPKVVLY SEDVDIETPD THISYMPTIK EGNSRELMGQ QSM PNRPNY IAFRDNFIGL MYYNSTGNMG VLAGQASQLN AVVDLQDRNT ELSYQLLLDS IGDRTRYFSM WNQAVDSYDP DVRI IENHG TEDELPNYCF PLGGVINTET LTKVKPKTGQ ENGWEKDATE FSDKNEIRVG NNFAMEINLN ANLWRNFLYS NIALY LPDK LKYSPSNVKI SDNPNTYDYM NKRVVAPGLV DCYINLGARW SLDYMDNVNP FNHHRNAGLR YRSMLLGNGR YVPFHI QVP QKFFAIKNLL LLPGSYTYEW NFRKDVNMVL QSSLGNDLRV DGASIKFDSI CLYATFFPMA HNTASTLEAM LRNDTND QS FNDYLSAANM LYPIPANATN VPISIPSRNW AAFRGWAFTR LKTKETPSLG SGYDPYYTYS GSIPYLDGTF YLNHTFKK V AITFDSSVSW PGNDRLLTPN EFEIKRSVDG EGYNVAQCNM TKDWFLVQML ANYNIGYQGF YIPESYKDRM YSFFRNFQP MSRQVVDDTK YKDYQQVGIL HQHNNSGFVG YLAPTMREGQ AYPANFPYPL IGKTAVDSIT QKKFLCDRTL WRIPFSSNFM SMGALTDLG QNLLYANSAH ALDMTFEVDP MDEPTLLYVL FEVFDVVRVH RPHRGVIETV YLRTPFSAGN ATT

UniProtKB: Hexon protein

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Macromolecule #2: Prothrombin

MacromoleculeName: Prothrombin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: thrombin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.56293 KDa
SequenceString: MAHVRGLQLP GCLALAALCS LVHSQHVFLA PQQARSLLQR VRRANTFL(CGU)(CGU) VRKGNL(CGU)R(CGU)C V (CGU)(CGU)TCSY(CGU)(CGU) AF(CGU)AL(CGU)SSTA TDVFWAKYTA CETARTPRDK LAACLEGNCA EGLGTNYR G HVNITRSGIE ...String:
MAHVRGLQLP GCLALAALCS LVHSQHVFLA PQQARSLLQR VRRANTFL(CGU)(CGU) VRKGNL(CGU)R(CGU)C V (CGU)(CGU)TCSY(CGU)(CGU) AF(CGU)AL(CGU)SSTA TDVFWAKYTA CETARTPRDK LAACLEGNCA EGLGTNYR G HVNITRSGIE CQLWRSRYPH KPEINSTTHP GADLQENFCR NPDSSTTGPW CYTTDPTVRR QECSIPVCGQ DQVTVAMTP RSEGSSVNLS PPLEQCVPDR GQQYQGRLAV TTHGLPCLAW ASAQAKALSK HQDFNSAVQL VENFCRNPDG DEEGVWCYVA GKPGDFGYC DLNYCEEAVE EETGDGLDED SDRAIEGRTA TSEYQTFFNP RTFGSGEADC GLRPLFEKKS LEDKTERELL E SYIDGRIV EGSDAEIGMS PWQVMLFRKS PQELLCGASL ISDRWVLTAA HCLLYPPWDK NFTENDLLVR IGKHSRTRYE RN IEKISML EKIYIHPRYN WRENLDRDIA LMKLKKPVAF SDYIHPVCLP DRETAASLLQ AGYKGRVTGW GNLKETWTAN VGK GQPSVL QVVNLPIVER PVCKDSTRIR ITDNMFCAGY KPDEGKRGDA CEGDSGGPFV MKSPFNNRWY QMGIVSWGEG CDRD GKYGF YTHVFRLKKW IQKVIDQFGE

UniProtKB: Prothrombin

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 7 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.2 / Component - Concentration: 20.0 mM / Component - Name: Hepes
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 3 / Number real images: 10000 / Average electron dose: 81.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 59000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6b1t

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2324
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationSoftware - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6b1t


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9cln:
Cryo-EM model derived from localized reconstruction of human adenovirus 5 (Ad5)-hexon-FII complex at 3.9A resolution

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