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- PDB-9fah: Human adenovirus type 37 fiber knob in complex with 4-O,5-N-diace... -

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Open data


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Basic information

Entry
Database: PDB / ID: 9fah
TitleHuman adenovirus type 37 fiber knob in complex with 4-O,5-N-diacetylneuraminic 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 / metal ion binding
Similarity search - Function
Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
ACETATE ION / Chem-ANA / Fiber
Similarity search - Component
Biological speciesHuman adenovirus D37
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65336537283 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)122,19020
Polymers120,2593
Non-polymers1,93117
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-178 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.881, 66.726, 73.949
Angle α, β, γ (deg.)90.000, 97.747, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNTHRTHR(chain A and ((resid 181 and (name O or name...AA181 - 185181 - 185
12TRPTRPPROPRO(chain A and ((resid 181 and (name O or name...AA187 - 296187 - 296
13SERSERILEILE(chain A and ((resid 181 and (name O or name...AA299 - 337299 - 337
14PHEPHEGLUGLU(chain A and ((resid 181 and (name O or name...AA339 - 365339 - 365
21ASNASNTHRTHR(chain C and ((resid 181 and (name N or name...CC181 - 185181 - 185
22TRPTRPPROPRO(chain C and ((resid 181 and (name N or name...CC187 - 296187 - 296
23SERSERILEILE(chain C and ((resid 181 and (name N or name...CC299 - 337299 - 337
24PHEPHEGLUGLU(chain C and ((resid 181 and (name N or name...CC339 - 365339 - 365

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Fiber


Mass: 40086.266 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D37 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q64823
#2: Sugar ChemComp-ANA / methyl 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / 4-O-ACETYL-ALPHA-2-OMETHYL-5-N-ACETYL-ALPHA-D-NEURAMINIC ACID / methyl 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid / methyl 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosidonic acid / methyl 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosidonic acid


Type: D-saccharide / Mass: 365.333 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H23NO10 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
4-O-acetyl-2-O-methyl-5-N-acetyl-a-D-neuraminic acidIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 286 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 293 K / Method: vapor diffusion, hanging drop
Details: 26% PEG 8000, 0.1 M HEPES pH 6.9, 0.05 M zinc acetate

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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: 1.65→50 Å / Num. obs: 65451 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.331140676 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.8
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 6.9 % / Num. unique obs: 10438 / CC1/2: 0.495 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65336537283→47.9040909403 Å / SU ML: 0.199489811402 / Cross valid method: FREE R-VALUE / σ(F): 1.36673149348 / Phase error: 20.4086590016
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.190329875849 3273 5.00068753724 %
Rwork0.157671212129 62178 -
obs0.159336092102 65451 99.7227004708 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.7471423124 Å2
Refinement stepCycle: LAST / Resolution: 1.65336537283→47.9040909403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4234 0 113 272 4619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01000018704614442
X-RAY DIFFRACTIONf_angle_d1.055710633296051
X-RAY DIFFRACTIONf_chiral_restr0.0708199743502699
X-RAY DIFFRACTIONf_plane_restr0.00736903992421764
X-RAY DIFFRACTIONf_dihedral_angle_d12.1001271762613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6534-1.6780.318567524261350.3032216976352576X-RAY DIFFRACTION95.323488045
1.678-1.70430.3505842216161410.2834070689282683X-RAY DIFFRACTION100
1.7043-1.73220.2968855111661430.2622731248672702X-RAY DIFFRACTION100
1.7322-1.76210.3025619145421410.2504488418362697X-RAY DIFFRACTION99.9647763297
1.7621-1.79410.3109640148911420.2360213769692693X-RAY DIFFRACTION99.9647390691
1.7941-1.82860.2633870168661410.2120330061862679X-RAY DIFFRACTION100
1.8286-1.8660.2524955766261430.2031211119922712X-RAY DIFFRACTION99.9299964998
1.866-1.90650.221879997331440.1884058896062731X-RAY DIFFRACTION99.9652294854
1.9065-1.95090.229156788981410.1956916491592677X-RAY DIFFRACTION99.8936547324
1.9509-1.99970.19436781531400.1615019756272672X-RAY DIFFRACTION99.9644507643
1.9997-2.05370.1995493959151430.1475443270642714X-RAY DIFFRACTION99.9300454704
2.0537-2.11420.213710386641430.1566102764472714X-RAY DIFFRACTION99.9650104969
2.1142-2.18240.1901395202441420.1550922522632700X-RAY DIFFRACTION100
2.1824-2.26040.2044068646031420.1536208348522692X-RAY DIFFRACTION99.6483825598
2.2604-2.35090.20030819531430.1551478447832707X-RAY DIFFRACTION99.9298737728
2.3509-2.45790.1964439244221420.1575971652512697X-RAY DIFFRACTION100
2.4579-2.58750.1957811268831440.1605860869172735X-RAY DIFFRACTION100
2.5875-2.74960.2017426755891420.1564537535222700X-RAY DIFFRACTION100
2.7496-2.96180.1994507254921420.1601677773362710X-RAY DIFFRACTION99.9299229152
2.9618-3.25990.2009078032071440.1555377970192724X-RAY DIFFRACTION99.9303135889
3.2599-3.73140.1583009829121430.1376273021832724X-RAY DIFFRACTION99.6870653686
3.7314-4.70050.1302933786261440.12264545252742X-RAY DIFFRACTION99.6546961326
4.7005-47.90409094030.1862038367941480.1563768838752797X-RAY DIFFRACTION99.9321343739
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)
10.3783585778240.51925840009-0.2678505309420.941397557982-0.2485387128530.946668171681-0.04877088064050.140321338948-0.105864028107-0.01651669277730.0414744246840.06727352813980.369578134335-0.0610545866233-0.01146793479590.215870173284-0.0151165036113-0.01658037895880.193173390514-0.006079061046020.215038841364-3.67471963417-10.305799608419.5790499211
20.60888192860.108820455203-0.567090443290.5248933354190.04286388866230.3172993530870.07406495099450.2487385710170.1093671291150.343794291242-0.02336433314350.343733472009-0.0814800401026-0.1396066693930.01213891097730.2051930755470.0001872678695270.02425003818160.248409067260.06029355921130.281276027866-10.133994904-4.4228410451425.6048013373
30.7536907214180.152880678441-0.4086258438620.234319965792-0.04281775273090.177708056428-0.135589057807-0.150303640544-0.276989653844-0.03443019329340.0509686788768-0.0775216133140.09204841676180.07895559491690.000109877665030.337783574140.01720658554240.01853931567060.1908461768350.04001341325180.282200879271.82750090096-16.465181928530.1760915087
40.9190155201240.220721463524-0.03950644258621.00213438306-0.01030276798070.240125374440.0360461716952-0.02662113245220.1049087928240.1467885314690.08079399714650.211399511917-0.11585144419-0.05122202757280.0001395584208280.2012859025510.02207302433290.02408865136420.1649141911190.01499724874860.198892971361-2.603341458442.9715174394324.3363708326
50.06097335886110.1434534654570.1162905522860.2946205939140.2741659300930.467348023695-0.1196956415350.4714315083250.0102940540122-0.3209620823570.1804538977460.04797323364530.358435975952-0.316564522539-0.08435752753230.188610703644-0.0933468185044-0.07727448809050.3325234467150.09210075473640.198702454999-7.92479127248-2.567156846847.80819296695
60.1843077358980.06675878182910.002051125343480.1305159140760.05275896238630.03399089738210.14041363927-0.128367559003-0.07158576749370.104498216888-0.03071534413480.2156758111490.247014572787-0.002529517387410.000806356180160.2240184764820.0219037282205-0.01863110513270.199713947873-0.006326389501220.2072425320327.43054933644-3.8511794539628.7275599292
70.2708811784840.1658060391590.3732244757680.3272475127160.1663868518790.968518290268-0.3484275195880.172223216716-0.110667867095-0.1333351057110.217625311107-0.460034781644-0.07192720956230.8859463270670.04233735038770.2880491366490.1540775840720.0518008781770.528878887006-0.0002722596441790.33617115886626.7035822254-4.496372002524.03343090517
81.05521363444-0.0354826169628-0.2442695547210.7120358926280.6599175400970.920220046094-0.05528531394610.220111628919-0.103009422253-0.175655354686-0.0931138053024-0.1016864362070.144465032990.330331107886-0.02255879841360.2561666450550.05532571880470.02484973664540.2706812377330.005212590774470.20563383417618.4106784029-3.303229175652.22342140081
90.1134785500010.0953235624449-0.05481105106630.2668846436790.1224268927610.144453602769-0.08813708341370.0184120234088-0.3507212827320.2680483374140.0662468897517-0.3276862159020.3509709880020.4815054711980.012496447290.360763645420.1996578004720.0692632904940.4662685033370.006074985301330.4153012474625.3732463626-14.607197104710.0986672752
100.6871297776630.313980139829-0.4515824893390.35314816864-0.05560980406651.11934958562-0.09533045773720.210083700369-0.0275846135831-0.149315710340.005145454559040.002748382274820.1814771690870.0621062000233-0.0006914954739590.2461855186380.0120553709824-0.009637227424810.204003987396-0.003459642337540.21056387982310.6598829775-2.886724852685.69637309313
110.2078096536320.0937450520207-0.1091946678820.1931697560230.04352750723720.0858111421603-0.0415292429541-0.462323498395-0.05448522746730.366530338807-0.03421530019390.2266908698150.1771499164990.3343206701670.0008294179140150.2937268375170.0503486184675-0.0466920505680.384138638452-0.03304254757370.25946404655117.67601673432.8819575815837.3866519572
121.305571480370.0208499085552-0.4354682408820.385476371923-0.286458714771.426160880470.0824236166252-0.1860183498560.1304869791820.226352583735-0.00231656767676-0.131164394027-0.2182554875470.3331301650730.0007593016088360.215889107281-0.034851295593-0.02123647847750.22779727-0.04787150784430.21528883372617.363828208514.440077671429.9073042431
130.1369007101110.0674858663978-0.01767333921990.1036601307180.001539437020380.161513660058-0.0644776878473-0.550348961803-0.1264527963910.3733640742380.0694702350149-0.1880907290350.04441324384310.185455395882-2.07806105175E-50.3947139708140.0554426723372-0.09035269959050.587210841407-0.009567141491690.33566132615223.68865910951.6942027600539.5715340214
140.3430724945170.2641617474820.4573497801020.303785441190.3493753104320.491705021275-0.08127591196950.06833772404620.04898765317940.07427846889550.110107964692-0.0629596074334-0.09765001364890.3263163503970.0042546976990.1225166334360.0168247341837-0.001549119538230.3134119779240.0293136198610.22309332249623.60478787588.3401751626817.1025454788
150.0316416796879-0.257045010782-0.1995451269420.6773983784120.008999081728860.8431605298340.06520014112860.09216934624250.1090827663090.0879809738024-0.0231465485063-0.143987224544-0.2417860056690.210795256779-2.79870662944E-50.200033494417-0.007548979457160.001259323786930.2224447996360.01633789406090.26769941801816.01151165214.917178293721.6158467875
160.1191568279670.2234207384470.1058559433620.281591081449-0.03961987961310.814617621325-0.00475487910161-0.0749838488257-0.009547747623380.1383502933260.006019484552420.0837725868498-0.1472280060770.2381536024270.001873435613370.2007914850170.01171323627970.0079053258870.196106888115-0.008976178996240.21387734587812.93102577859.1540203569525.1561920745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 182 through 234 )
2X-RAY DIFFRACTION2chain 'A' and (resid 235 through 263 )
3X-RAY DIFFRACTION3chain 'A' and (resid 264 through 291 )
4X-RAY DIFFRACTION4chain 'A' and (resid 292 through 347 )
5X-RAY DIFFRACTION5chain 'A' and (resid 348 through 356 )
6X-RAY DIFFRACTION6chain 'A' and (resid 357 through 365 )
7X-RAY DIFFRACTION7chain 'B' and (resid 183 through 203 )
8X-RAY DIFFRACTION8chain 'B' and (resid 204 through 263 )
9X-RAY DIFFRACTION9chain 'B' and (resid 264 through 286 )
10X-RAY DIFFRACTION10chain 'B' and (resid 287 through 365 )
11X-RAY DIFFRACTION11chain 'C' and (resid 180 through 197 )
12X-RAY DIFFRACTION12chain 'C' and (resid 198 through 263 )
13X-RAY DIFFRACTION13chain 'C' and (resid 264 through 283 )
14X-RAY DIFFRACTION14chain 'C' and (resid 284 through 315 )
15X-RAY DIFFRACTION15chain 'C' and (resid 316 through 347 )
16X-RAY DIFFRACTION16chain 'C' and (resid 348 through 365 )

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