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- PDB-9fag: Human adenovirus type 36 fiber knob in complex with 4,9-O,5-N-tri... -

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Basic information

Entry
Database: PDB / ID: 9fag
TitleHuman adenovirus type 36 fiber knob in complex with 4,9-O,5-N-triacetylneuraminic acid
ComponentsFiber
KeywordsVIRAL PROTEIN / fiber knob / complex / sialic acid
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Chem-SIO / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 36
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStrebl, M. / Liaci, A.M. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: Plos Pathog. / Year: 2025
Title: Extended receptor repertoire of an adenovirus associated with human obesity.
Authors: Liaci, A.M. / Chandra, N. / Vodnala, S.M. / Strebl, M. / Kumar, P. / Pfenning, V. / Bachmann, P. / Caraballo, R. / Chai, W. / Johansson, E. / Elofsson, M. / Feizi, T. / Liu, Y. / Stehle, T. / Arnberg, N.
History
DepositionMay 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fiber
B: Fiber
C: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,13910
Polymers120,4923
Non-polymers1,6477
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-22 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.591, 99.208, 111.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Fiber


Mass: 40164.016 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 36 / Production host: Escherichia coli (E. coli) / References: UniProt: D4N3K6
#2: Sugar ChemComp-SIO / methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / methyl 4,9-di-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid / methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosidonic acid / methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosidonic acid


Type: D-saccharide, alpha linking / Mass: 407.370 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H25NO11 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 26% PEG 3350, 175 mM NH4Ac, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 52253 / % possible obs: 99.4 % / Redundancy: 13.4 % / Biso Wilson estimate: 26.62728689 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 13 % / Num. unique obs: 8111 / CC1/2: 0.532 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.4501235152 Å / SU ML: 0.259094853354 / Cross valid method: FREE R-VALUE / σ(F): 1.33305318081 / Phase error: 21.9330095151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206181073136 2613 5.000669818 %
Rwork0.169145076016 49640 -
obs0.171058499383 52253 99.9502668375 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.7680285991 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.4501235152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4241 0 112 281 4634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01053531491844576
X-RAY DIFFRACTIONf_angle_d1.124135760676254
X-RAY DIFFRACTIONf_chiral_restr0.0670388485514717
X-RAY DIFFRACTIONf_plane_restr0.00637027902106790
X-RAY DIFFRACTIONf_dihedral_angle_d12.33424724012707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93910.4609260098431350.4199079837352577X-RAY DIFFRACTION99.7792494481
1.9391-1.97640.3267307769831350.2807738905472559X-RAY DIFFRACTION100
1.9764-2.01670.2482829034551350.2236566786372572X-RAY DIFFRACTION100
2.0167-2.06060.2435351574171370.2130467741552601X-RAY DIFFRACTION100
2.0606-2.10850.2803022891591360.2096802073372574X-RAY DIFFRACTION100
2.1085-2.16120.2524708302011350.200478595952568X-RAY DIFFRACTION100
2.1612-2.21970.22870512641370.1962819971862599X-RAY DIFFRACTION99.926953981
2.2197-2.2850.3038280443381350.2409086902092579X-RAY DIFFRACTION99.6328928047
2.285-2.35870.2185464980571370.1796759624252594X-RAY DIFFRACTION100
2.3587-2.4430.2325788984281350.1770144739552573X-RAY DIFFRACTION100
2.443-2.54080.247267614431380.1662477575342608X-RAY DIFFRACTION100
2.5408-2.65650.2032814777051360.1607524612552592X-RAY DIFFRACTION100
2.6565-2.79650.2256338085671380.1596564287232616X-RAY DIFFRACTION100
2.7965-2.97170.2229400201171380.1645315743242633X-RAY DIFFRACTION99.9639249639
2.9717-3.20110.2125968188811380.1613314363962624X-RAY DIFFRACTION100
3.2011-3.52320.1712891900991390.1469844592532635X-RAY DIFFRACTION99.963963964
3.5232-4.03280.1590030537241390.1391934450762637X-RAY DIFFRACTION99.9639899172
4.0328-5.080.1402216760441410.1197037103582687X-RAY DIFFRACTION99.9646518204
5.08-48.450.1947521729081490.1678940345512812X-RAY DIFFRACTION99.8650927487
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.17059692565-2.67284670096-0.04706224886564.93374124756-0.0472308658633.395639744020.09051980058620.326775226362-0.0339082085138-0.221044601696-0.119399222362-0.02821914715140.132155019747-0.0345654285296-0.02352632264930.297153799087-0.04297154324160.001193185055010.292913244672-0.05556651549050.218227310199-9.929803571834.07178462582-30.8955848854
23.52370987082-1.430453084110.9521376372863.10452922982-0.1141542334731.82064516440.01371530145370.2418124804060.159934687909-0.0448252026695-0.152878894863-0.2570553446220.04697496873680.02184744923450.1338266688430.197398866952-0.01156924962760.004091520843020.18070442127-0.0280753979750.180295289794-6.394234733452.58646590875-22.5821364288
31.6477779207-0.634256405714-0.3579842318472.478458060882.419768701052.42728445369-0.03143123227610.08221216507050.03252888204850.183628348885-0.1654089182630.3583540307850.0187033968151-0.3365935853280.178510161690.2031572184720.00171671457461-0.0472690403520.292061563005-0.02437372728350.245284502428-21.807251485111.0265793939-20.6316680641
41.56972625063-0.710092660555-0.5323016686593.44158266132-0.9793830631332.189948790750.005732610392790.134656779193-0.142038255598-0.2100612987730.01871784033140.1613428578850.381441365807-0.210932155528-0.03272048936920.253313073853-0.0195688495759-0.04106927944260.241603473187-0.06601012997870.204218872439-13.4156329946-4.04334932461-31.4579323365
52.238210437110.8044291033242.511954026321.408676557982.416622300034.85811979484-0.1088527944720.43909676151-0.128106609119-0.4598445276260.0134476763485-0.1066909327540.2216537154320.3921632124710.1573807517680.3519888946840.05912287118190.01953415134270.293609244276-0.05311209960450.287933906091-4.21260383339-6.78957170783-33.3507588006
65.615287427961.76709556668-2.965821825783.72322916066-2.554538336827.994721867590.0340506955082-0.0316702171747-0.4679498838590.007377374755890.01609552690830.711014184265-0.00298606183896-0.4123873210080.006482428473760.35264404063-0.06037552632710.03202577417550.2573728157070.007398597299710.447214626592-15.4845261956-13.3587666824-12.7334238585
71.65106097903-0.1428326313360.1137177211422.177497183190.5287921350612.065698776190.0289205129721-0.0743536255858-0.2575460588460.168071734914-0.06498263950020.06708249845160.289650824142-0.255784730450.0119731247150.206156296122-0.0417063663105-9.50771262863E-50.21963781764-0.01188783494440.223710076725-15.22128553210.862878711163-13.6298893789
84.72615057945-1.78843915576-1.15393677552.488063475570.5491577274444.00103493018-0.080225926555-0.07882614617630.0264122289187-0.1791649625520.146833545699-0.00876857276314-0.403489121661-0.175291323231-0.07432791706920.1982621483690.0276804903161-0.04888950823120.216249967786-0.04432036207240.173212526372-16.412675627119.2422240796-15.4963403551
95.582441113112.649949895781.569858018813.36099857442-0.2135161746413.285623221420.04476175877440.0827932500811-0.474811476543-0.05631899618410.0469247651919-0.312581914690.6762623446880.164842560872-0.05444287735930.2264104477740.006033017560550.02305430895740.154737883956-0.02043577200460.138253999606-5.62048875276-5.54133707199-16.7748825678
105.136155643230.651238114570.3356503708752.089518666570.3213211378273.441825171450.233705973262-0.124769724125-0.2617751814280.317971738882-0.0731825756434-0.6687210836870.4988086268490.0399841934703-0.1365113626660.2116006202730.00232890502698-0.003244193871580.364684848794-0.001212807982330.33159758575116.99761441347.90104067632-11.237300688
111.707733771910.391473179869-0.1521741660512.233538083281.463460377352.424410891920.0205503376794-0.02398360355510.1623002387540.0658957583960.0483948091896-0.09877628813230.00140407447910.262187982347-0.08249020430960.190939308934-0.00598791671381-0.008891700348930.240923713834-0.01027685448110.2150696256879.7883317093416.6256430862-6.18436637761
122.88758563548-1.11083972711-1.150289349282.896382988142.196159808783.12068353656-0.05766643060690.06149517129390.0259574598028-0.04391908188850.19187512352-0.215287549414-0.1606914218040.396235919974-0.1463825808370.151167850095-0.05415115542220.01520291750640.277222740803-0.01592043218490.22680542554316.058149169115.5125437171-17.2030160213
138.518214544310.3604679896571.461191800992.618957452360.7973404150012.91236659818-0.05375659142180.460216277001-0.101878154447-0.3067118976960.144232489333-0.287670042598-0.1677024746520.510610084298-0.05683793207880.25445186491-0.04868096847550.06114719928190.340826553611-0.03850890404960.17720998009311.749358460810.233078933-25.1652934126
141.831857732280.134198960047-0.01884422477760.6899623110320.5786173108882.7124791461-0.0008983852026330.1881497842790.167151637359-0.1265974723570.0590092444282-0.000963512595143-0.1250706384610.0238051053765-0.04453318555980.175150131204-0.0107748223025-0.00617635523470.1592467267920.005965315676560.1862026547960.74907682134416.5907884363-14.4946593833
150.8836347326830.7058443753531.475365742762.234366576881.114656969893.310852501550.0621796327161-0.03854809595140.03371535843070.189251183190.0598327972977-0.03942806806430.262741041540.242176718129-0.1775160431360.144257853956-0.0322451471670.002115561797830.209168120296-0.01427883590130.2395783781192.8703493701713.7569314707-6.27634951226
163.921757345210.485776299672-1.038438440964.860034891541.085223549242.57522163418-0.1627447264040.0858876549884-0.298124911244-0.1363184746920.3165907109920.04934137762331.259657235-0.05459145171-0.03935852558320.4256235179040.0149090603804-0.02585586673860.2404065558530.03518197016320.28312885445-3.00630126333-15.1496892095-4.68344156333
174.675956073360.685231468635-2.813235586282.14666138957-0.3758524704344.46940841925-0.1171924749350.06808700624410.01357250437410.1239362582180.143621107077-0.03945310997670.461680066465-0.05214226481310.02970459991390.2823583165380.0287865754151-0.03885686673870.179160128418-0.006095026029640.215702096715-3.09649114995-8.77964019719-2.49808970991
184.08138454827-1.0898298358-1.440435145551.224397053420.5317360542632.11770724778-0.0153283714245-0.267505456586-0.2058093938860.1316522242120.0225565423441-0.1416939110620.3330965418170.1276287389910.003477155690670.3435760382960.0110296503075-0.01876959192110.2488957134440.05999538150610.249647242237-4.07493818251-7.752624194897.75231059716
195.16748541090.2548301566520.942739351055.42543936326-1.941839824335.16261828274-0.05415761433810.129009370061-0.827879691789-0.6622657090620.300761730459-0.3723682299410.7454751199060.166548345492-0.2402767095780.5659905507530.1175251247860.01730339628690.2322591595710.002091632222760.4778475520734.56782652228-19.4944579302-5.29674048305
202.4764940437-0.3491905290790.01284033584761.57711678546-0.0613850639251.954512996470.015817372681-0.2595566945490.02019968576060.2075516907740.0118831889148-0.2639318081510.1228081118370.28659735966-0.02007690717270.2268111026690.00363440386826-0.03319238420490.2198705791810.005953894339140.1948091534393.471636144880.8047247832531.80767968748
212.813221593640.355117943916-0.9344389389231.17965546541-0.4416667058392.81244992847-0.0755495430057-0.0471341922717-0.235360892930.0945258900960.01630146126450.0007543786301020.152113383376-0.1212062093620.06906681015110.204447281273-0.00702752242822-0.03242630800180.1129897667690.01813571670820.140318942668-8.10929655757-0.0508434592987-0.521129886979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 179 through 200 )
2X-RAY DIFFRACTION2chain 'A' and (resid 201 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 245 )
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 264 )
5X-RAY DIFFRACTION5chain 'A' and (resid 265 through 281 )
6X-RAY DIFFRACTION6chain 'A' and (resid 282 through 298 )
7X-RAY DIFFRACTION7chain 'A' and (resid 299 through 347 )
8X-RAY DIFFRACTION8chain 'A' and (resid 348 through 362 )
9X-RAY DIFFRACTION9chain 'A' and (resid 363 through 371 )
10X-RAY DIFFRACTION10chain 'B' and (resid 179 through 194 )
11X-RAY DIFFRACTION11chain 'B' and (resid 195 through 237 )
12X-RAY DIFFRACTION12chain 'B' and (resid 238 through 265 )
13X-RAY DIFFRACTION13chain 'B' and (resid 266 through 291 )
14X-RAY DIFFRACTION14chain 'B' and (resid 299 through 347 )
15X-RAY DIFFRACTION15chain 'B' and (resid 348 through 371 )
16X-RAY DIFFRACTION16chain 'C' and (resid 180 through 194 )
17X-RAY DIFFRACTION17chain 'C' and (resid 195 through 222 )
18X-RAY DIFFRACTION18chain 'C' and (resid 223 through 258 )
19X-RAY DIFFRACTION19chain 'C' and (resid 259 through 278 )
20X-RAY DIFFRACTION20chain 'C' and (resid 279 through 347 )
21X-RAY DIFFRACTION21chain 'C' and (resid 348 through 371 )

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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