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- EMDB-45675: Cryo-EM model derived from localized reconstruction of human aden... -

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Basic information

Entry
Database: EMDB / ID: EMD-45675
TitleCryo-EM model derived from localized reconstruction of human adenovirus (Ad5)-hexon-FX complex at 3.6A resolution
Map data
Sample
  • Complex: Human adenovirus 5 (Ad5) in complex with Coagulation factor FX
    • Organelle or cellular component: Hexon protein
      • Organelle or cellular component: Human Coagulation Factor X
        • Protein or peptide: Coagulation factor X
      • 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 / coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / microtubule-dependent intracellular transport of viral material towards nucleus / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus ...T=25 icosahedral viral capsid / coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / microtubule-dependent intracellular transport of viral material towards nucleus / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / viral capsid / host cell / positive regulation of cell migration / symbiont entry into host cell / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / host cell nucleus / structural molecule activity / proteolysis / extracellular space / 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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla 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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like 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. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
Coagulation factor X / Hexon protein
Similarity search - Component
Biological speciesHuman adenovirus 5 / human blood metagenome (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 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_45675.png

Downloads & links

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Map

FileDownload / File: emd_45675.map.gz / Format: CCP4 / Size: 4.3 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 83 pix.
= 205.568 Å		1.41 Å/pix.
x 92 pix.
= 116.864 Å		1.41 Å/pix.
x 146 pix.
= 129.536 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: 0.01
Minimum - Maximum-0.09115553 - 0.16055463
Average (Standard dev.)0.0026619553 (±0.015622816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-38-49-40
Dimensions9214683
Spacing8314692
CellA: 116.864 Å / B: 205.568 Å / C: 129.536 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45675_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_45675_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 FX

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

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

SupramoleculeName: Human adenovirus 5 (Ad5) in complex with Coagulation factor FX
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: 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 X

SupramoleculeName: Human Coagulation Factor X / type: organelle_or_cellular_component / ID: 3 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: human blood metagenome (others)

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Macromolecule #1: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 1 / Details: Adenovirus hexon protein / 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: Coagulation factor X

MacromoleculeName: Coagulation factor X / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: coagulation factor Xa
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.286738 KDa
SequenceString: MGRPLHLVLL SASLAGLLLL GESLFIRREQ ANNILARVTR ANSFL(CGU)(CGU)MKK GHL(CGU)R(CGU)CM(CGU) (CGU)TCSY(CGU)(CGU)AR(CGU) VF(CGU)DSDKTN(CGU) FWNKYKDGDQ CETSPCQNQG KCKDGLGEYT CTCLEG FEG KNCELFTRKL ...String:
MGRPLHLVLL SASLAGLLLL GESLFIRREQ ANNILARVTR ANSFL(CGU)(CGU)MKK GHL(CGU)R(CGU)CM(CGU) (CGU)TCSY(CGU)(CGU)AR(CGU) VF(CGU)DSDKTN(CGU) FWNKYKDGDQ CETSPCQNQG KCKDGLGEYT CTCLEG FEG KNCELFTRKL CSLDNGDCDQ FCHEEQNSVV CSCARGYTLA DNGKACIPTG PYPCGKQTLE RRKRSVAQAT SSSGEAP DS ITWKPYDAAD LDPTENPFDL LDFNQTQPER GDNNLTRIVG GQECKDGECP WQALLINEEN EGFCGGTILS EFYILTAA H CLYQAKRFKV RVGDRNTEQE EGGEAVHEVE VVIKHNRFTK ETYDFDIAVL RLKTPITFRM NVAPACLPER DWAESTLMT QKTGIVSGFG RTHEKGRQST RLKMLEVPYV DRNSCKLSSS FIITQNMFCA GYDTKQEDAC QGDSGGPHVT RFKDTYFVTG IVSWGEGCA RKGKYGIYTK VTAFLKWIDR SMKTRGLPKA KSHAPEVITS SPLK

UniProtKB: Coagulation factor X

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
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: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26000
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-9cli:
Cryo-EM model derived from localized reconstruction of human adenovirus (Ad5)-hexon-FX complex at 3.6A resolution

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