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- EMDB-53736: Human Adenovirus D 10 Capsid Structure -

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Basic information

Entry
Database: EMDB / ID: EMD-53736
TitleHuman Adenovirus D 10 Capsid Structure
Map dataAdditional map of asymmetric unit of adenovirus capsid. Sharpened using phenix autosharpen and used for model building. Note this map does not share Cartesian coordinates with the primary or raw maps.
Sample
  • Virus: Human adenovirus D10
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: Hexon-interlacing protein
Keywordsvirus / adenovirus / capsid / conjunctivitis
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell / host cell cytoplasm ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell / host cell cytoplasm / endocytosis involved in viral entry into host cell / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus Pll, hexon, subdomain 3 / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI ...Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus Pll, hexon, subdomain 3 / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / 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 / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Hexon protein / Pre-hexon-linking protein VIII / Hexon-interlacing protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-protein VI
Similarity search - Component
Biological speciesHuman adenovirus D10
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWaraich K / Mundy RM / Bates EA / da Fonseca P / Morris E / Rizkallah PJ / Baker AT / Young MT / Parker AL / Bhella D
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: Identification of a novel structural motif and overexpression of key transcripts elucidated in Adenovirus 10
Authors: Mundy RM / Waraich K / Bates EA / Rizkallah PJ / Baker AT / Young MT / Morris E / da Fonseca PCA / Bliss CM / Matthews D / Bhella D / Parker AL
History
DepositionMay 14, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53736.png

Downloads & links

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Map

FileDownload / File: emd_53736.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAdditional map of asymmetric unit of adenovirus capsid. Sharpened using phenix autosharpen and used for model building. Note this map does not share Cartesian coordinates with the primary or raw maps.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 720 pix.
= 1193.76 Å		1.66 Å/pix.
x 720 pix.
= 1193.76 Å		1.66 Å/pix.
x 720 pix.
= 1193.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.658 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0216
Minimum - Maximum-0.09941467 - 0.11087721
Average (Standard dev.)0.0027774307 (±0.008876976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 1193.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional map of asymmetric unit of adenovirus capsid....

Fileemd_53736_additional_1.map
AnnotationAdditional map of asymmetric unit of adenovirus capsid. Sharpened using phenix autosharpen and used for model building. Note this map does not share Cartesian coordinates with the primary or raw maps.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2 from RELION Refine3D

Fileemd_53736_half_map_1.map
AnnotationHalf Map 2 from RELION Refine3D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1 from RELION Refine3D

Fileemd_53736_half_map_2.map
AnnotationHalf Map 1 from RELION Refine3D
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 D10

EntireName: Human adenovirus D10
Components
  • Virus: Human adenovirus D10
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: Hexon-interlacing protein

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Supramolecule #1: Human adenovirus D10

SupramoleculeName: Human adenovirus D10 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Propagation of viral stock in immortalised human cell line and purification by Caesium chloride density gradients.
NCBI-ID: 28275 / Sci species name: Human adenovirus D10 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Pre-protein VI

MacromoleculeName: Pre-protein VI / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus D10
Molecular weightTheoretical: 25.546086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEDINFASLA PRHGTRPFMG TWNEIGTSQL NGGAFNWSSV WSGLKNFGST LRTYGNKAWN SSTGQLLREK LKDQNFQQKV VDGLASGIN GVVDIANQAV QREINSRLDP RPPTVVEMED ATLPPPKGEK RPRPDAEETI LQVDEPPSYE EAVKAGMPTT R IIAPLATG ...String:
MEDINFASLA PRHGTRPFMG TWNEIGTSQL NGGAFNWSSV WSGLKNFGST LRTYGNKAWN SSTGQLLREK LKDQNFQQKV VDGLASGIN GVVDIANQAV QREINSRLDP RPPTVVEMED ATLPPPKGEK RPRPDAEETI LQVDEPPSYE EAVKAGMPTT R IIAPLATG VMKPATLDLP PPPAPAPPKA TPVVQAPPVA TAVRRVPARR QAQNWQSTLH SIVGLGVKSL KRRRCY

UniProtKB: Pre-protein VI

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Macromolecule #2: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus D10
Molecular weightTheoretical: 106.26843 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMPQWAYMHI AGQDASEYLS PGLVQFARAT DTYFSLGNKF RNPTVAPTHD VTTDRSQRLT LRFVPVDRED TTYSYKARFT LAVGDNRVL DMASTYFDIR GVLDRGPSFK PYSGTAYNSL APKSAPNPSQ WTANEKQTGG QPKSVTQTFG SAPMGGSNIT I EGLVIGTK ...String:
MMPQWAYMHI AGQDASEYLS PGLVQFARAT DTYFSLGNKF RNPTVAPTHD VTTDRSQRLT LRFVPVDRED TTYSYKARFT LAVGDNRVL DMASTYFDIR GVLDRGPSFK PYSGTAYNSL APKSAPNPSQ WTANEKQTGG QPKSVTQTFG SAPMGGSNIT I EGLVIGTK EEEGNATEEI FADKTFQPEP QVGEENWQET EAFYGGRALK KDTKMKPCYG SFARPTNEKG GQAKLKLNDQ GQ PTKDYDI DLAFFDTPGG TPPTGSGQQE EYKADIVMYT ENVNLETPDT HVVYKPGKED ESSETNLTQQ SMPNRPNYIG FRD NFVGLM YYNSTGNMGV LAGQASQLNA VVDLQDRNTE LSYQLLLDSL GDRTRYFSMW NSAVDSYDPD VRIIENHGVE DELP NYCFP LNGTGTNSTY QGVKVKTGQD GAEETEWDKD ETVARQNQIA KGNVYAMEIN LQANLWKSFL YSNVALYLPD SYKYT PANV TLPANTNTYE YMNGRVVAPS LVDAYINIGA RWSLDPMDNV NPFNHHRNAG LRYRSMLLGN GRYVPFHIQV PQKFFA IKN LLLLPGSYTY EWNFRKDVNM ILQSSLGNDL RVDGASVRFD SVNLYATFFP MAHNTASTLE AMLRNDTNDQ SFNDYLS AA NMLYPIPAKA TNVPISIPSR NWAAFRGWSF TRLKTKETPS LGSGFDPYFV YSGSIPYLDG TFYLNHTFKK VSIMFDSS V SWPGNDRLLT PNEFEIKRSV DGEGYNVAQC NMTKDWFLVQ MLSHYNIGYQ GFHVPEGYKD RMYSFFRNFQ PMSRQVVDE INYKDYKAVT LPFQHNNSGF TGYLAPTMRQ GQPYPANFPY PLIGQTAVPS VTQKKFLCDR VMWRIPFSSN FMSMGALTDL GQNMLYANS AHALDMTFEV DPMDEPTLLY LLFEVFDVVR VHQPHRGVIE AVYLRTPFSA GN

UniProtKB: Hexon protein

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Macromolecule #3: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus D10
Molecular weightTheoretical: 58.631703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRRAVVSSSP PPSYESVMAQ ATLEVPFVPP RYMAPTEGRN SIRYSELAPQ YDTTRVYLVD NKSADIASLN YQNDHSNFLT TVVQNNDFT PAEASTQTIN FDERSRWGGD LKTILHTNMP NVNEYMFTSK FKARVMVARK HPEGVVETDL SQDKLEYEWF E FTLPEGNF ...String:
MRRAVVSSSP PPSYESVMAQ ATLEVPFVPP RYMAPTEGRN SIRYSELAPQ YDTTRVYLVD NKSADIASLN YQNDHSNFLT TVVQNNDFT PAEASTQTIN FDERSRWGGD LKTILHTNMP NVNEYMFTSK FKARVMVARK HPEGVVETDL SQDKLEYEWF E FTLPEGNF SETMTIDLMN NAILENYLQV GRQNGVLESD IGVKFDSRNF KLGWDPVTKL VMPGVYTYEA FHPDVVLLPG CG VDFTESR LSNLLGIRKK QPFQEGFRIM YEDLEGGNIP ALLDVPKYLE SKKKVEDETK NAAAATADTT TRGDTFATPA QET AADKKV EVLPIEKDES GRSYNLIQGT HDTLYRSWYL SYTYGDPEKG VQSWTLLTTP DVTCGAEQVY WSLPDLMQDP VTFR STQQV SNYPVVGAEL MPFRAKSFYN DLAVYSQLIR SYTSLTHVFN RFPDNQILCR PPAPTITTVS ENVPALTDHG TLPLR SSIR GVQRVTVTDA RRRTCPYVYK ALGIVAPRVL SSRTF

UniProtKB: Penton protein

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Macromolecule #4: Pre-hexon-linking protein IIIa

MacromoleculeName: Pre-hexon-linking protein IIIa / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus D10
Molecular weightTheoretical: 62.170395 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQQAPDPAIR AALQSQPSGI ASDDWEAAMQ RIMALTTRNP ESFRQQPQAN RLSAILEAVV PSRTNPTHEK VLAIVNALAE NKAIRPDEA GLVYNALLER VGRYNSTNVQ SNLDRLVTDV REAVAQRERF KNEGLGSLVA LNAFLATQPA NVPRGQDDYT N FISALRLM ...String:
MQQAPDPAIR AALQSQPSGI ASDDWEAAMQ RIMALTTRNP ESFRQQPQAN RLSAILEAVV PSRTNPTHEK VLAIVNALAE NKAIRPDEA GLVYNALLER VGRYNSTNVQ SNLDRLVTDV REAVAQRERF KNEGLGSLVA LNAFLATQPA NVPRGQDDYT N FISALRLM VTEVPQSEVY QSGPDYFFQT SRQGLQTVNL SQAFKNLRGL WGVQAPVGDR STVSSLLTPN SRLLLLLIAP FT DSGSVNR NSYLGHLLTL YREAIGQAQV DEQTFQEITS VSRALGQNDT DSLRATLNFL LTNRQQKIPA QYALSAEEER ILR YVQQSV GLFLMQEGAT PSAALDMTAR NMEPSMYAAN RPFINKLMDY LHRAAVMNTD YFTNAILNPH WLPPPGFYTG EYDM PDPND GFLWDDVDSV VFSPTFQKRQ EAPPSEGAVG RSPFPSLGSL HSLPGSVNSG RVSRPRLLGE DEYLNDSLLQ PPRAK NAMA NNGIESLVDK LNRWKTYAQD HRDAPAPRRQ RHDRQRGLVW DDEDSADDSS VLDLGGSGGV NPFAHLQPKL GRRMF

UniProtKB: Pre-hexon-linking protein IIIa

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Macromolecule #5: Pre-hexon-linking protein VIII

MacromoleculeName: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus D10
Molecular weightTheoretical: 24.660668 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKEIPTPYM WSYQPQMGLA AGASQDYSTR MNWLSAGPSM ISRVNGVRNH RNQILLEQAA VTSTPRAKLN PRNWPSTLVY QEIPGPTTV LLPRDALAEV RMTNSGVQLA GGASRCPLRP QSGIKTLVIR GRGTQLNDEL VSSSIGLRPD GVFQLAGAGR S SFTPNQAY ...String:
MSKEIPTPYM WSYQPQMGLA AGASQDYSTR MNWLSAGPSM ISRVNGVRNH RNQILLEQAA VTSTPRAKLN PRNWPSTLVY QEIPGPTTV LLPRDALAEV RMTNSGVQLA GGASRCPLRP QSGIKTLVIR GRGTQLNDEL VSSSIGLRPD GVFQLAGAGR S SFTPNQAY LTLQSSSSEP RSGGIGTLQF VEEFVPSVYF NPFSGSPGLY PDEFIPNFDA VREAVDGYD

UniProtKB: Pre-hexon-linking protein VIII

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Macromolecule #6: Hexon-interlacing protein

MacromoleculeName: Hexon-interlacing protein / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus D10
Molecular weightTheoretical: 13.773352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MNGTGGAFEG GLFSPYLTTR LPGWAGVRQN VMGSTVDGRP VLPANSSTMT YATVGSSSLD STAAAAAAAA AMTATRLASS YMPSSGSSP SVPSSIIAEE KLLALLAELE ALSRQLAALT QQVSELREQQ QQQNK

UniProtKB: Hexon-interlacing protein

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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

BufferpH: 7.4
Details: Phosphate Buffered Saline (PBS) 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 5524
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9r78:
Human Adenovirus D 10 Capsid Structure

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