PDB-9fae: Human adenovirus type 36 fiber knob in complex with 4-O-acetyl-3'...

ID or keywords:

Entry

Database: PDB / ID: 9fae

Title

Human adenovirus type 36 fiber knob in complex with 4-O-acetyl-3'-sialyllactose

Components

Fiber

Keywords

VIRAL 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

Biological species

Human adenovirus 36

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5735397337 Å

Authors

Strebl, M. / Liaci, A.M. / Pfenning, V. / Stehle, T.

Funding support

Germany, 1items

Citation

Journal: 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

Deposition	May 10, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 22, 2025	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2025	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9fae.cif.gz	298.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9fae.ent.gz	196.7 KB	Display	PDB format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fa/9fae ftp://data.pdbj.org/pub/pdb/validation_reports/fa/9fae	HTTPS FTP

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Related structure data

Related structure data	9fafC 9fagC 9fahC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#132 - Dec 2010 Adenovirus similarity (7)

Deposited unit

A: Fiber

B: Fiber

C: Fiber

hetero molecules

122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	51.129, 98.644, 99.826
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
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

#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: Polysaccharide

4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-3)-beta-D- ...

Type: oligosaccharide / Mass: 513.448 Da / Num. of mol.: 1 / Source method: obtained synthetically

#3: Sugar

ChemComp-PKM / 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / 4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid / 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid / 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosonic acid

Type: D-saccharide, alpha linking / Mass: 351.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₂₁NO₁₀ / Feature type: SUBJECT OF INVESTIGATION

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 3350, 185 mM NH4Ac, 0.1 M Bis-Tris pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.57→50 Å / Num. obs: 133755 / % possible obs: 98.8 % / Redundancy: 6.8 % / B_iso Wilson estimate: 25.4 Å² / CC_1/2: 0.999 / Net I/σ(I): 14
Reflection shell	Resolution: 1.57→1.67 Å / Redundancy: 6.3 % / Num. unique obs: 20662 / CC_1/2: 0.651 / % possible all: 94.3

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5735397337→45.50728515 Å / SU ML: 0.176920897141 / Cross valid method: FREE R-VALUE / σ(F): 1.3601203312 / Phase error: 17.6918432536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.187024423223	6671	4.98747710366 %
R_work	0.155110951343	127084	-
obs	0.156703663775	133755	98.8434821165 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 20.7588548491 Å²

Refinement step

Cycle: LAST / Resolution: 1.5735397337→45.50728515 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4331	0	83	463	4877

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0116399935378	4598
X-RAY DIFFRACTION	f_angle_d	1.24007137757	6304
X-RAY DIFFRACTION	f_chiral_restr	0.0769103769955	727
X-RAY DIFFRACTION	f_plane_restr	0.00799211881714	803
X-RAY DIFFRACTION	f_dihedral_angle_d	12.1716505067	2836

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5735397337-1.5914	0.303449116132	173	0.280865806696	3291	X-RAY DIFFRACTION	76.5524861878
1.5914-1.6101	0.280959825149	221	0.24074861053	4234	X-RAY DIFFRACTION	98.5619469027
1.6101-1.6298	0.273669385844	223	0.232401928614	4187	X-RAY DIFFRACTION	99.1679784124
1.6298-1.6504	0.27087973351	228	0.230264088988	4327	X-RAY DIFFRACTION	99.1726540388
1.6504-1.6721	0.26614903041	223	0.225383705338	4187	X-RAY DIFFRACTION	98.8789237668
1.6721-1.695	0.25237714002	222	0.217649430545	4247	X-RAY DIFFRACTION	99.0689425848
1.695-1.7193	0.218571129378	224	0.204485031555	4281	X-RAY DIFFRACTION	99.2072230786
1.7193-1.7449	0.247757348281	223	0.195041932524	4203	X-RAY DIFFRACTION	99.3936671907
1.7449-1.7722	0.243970137438	221	0.186362321655	4297	X-RAY DIFFRACTION	99.4278169014
1.7722-1.8012	0.247255856116	219	0.179079884051	4262	X-RAY DIFFRACTION	99.4231195917
1.8012-1.8323	0.218894800936	224	0.17073185885	4257	X-RAY DIFFRACTION	99.4893428064
1.8323-1.8656	0.198222607911	229	0.16350335717	4275	X-RAY DIFFRACTION	99.557913351
1.8656-1.9015	0.23311864193	222	0.163390098838	4264	X-RAY DIFFRACTION	99.5561473591
1.9015-1.9403	0.182473230746	227	0.163784615658	4247	X-RAY DIFFRACTION	99.6214651525
1.9403-1.9825	0.197615988939	226	0.158877079128	4294	X-RAY DIFFRACTION	99.6912218791
1.9825-2.0286	0.190009518748	226	0.146099170981	4277	X-RAY DIFFRACTION	99.7342192691
2.0286-2.0794	0.17459671949	228	0.151781976489	4273	X-RAY DIFFRACTION	99.778319663
2.0794-2.1356	0.201892749431	223	0.146420015622	4314	X-RAY DIFFRACTION	99.9119136754
2.1356-2.1984	0.176509819866	223	0.144001834443	4257	X-RAY DIFFRACTION	99.8885172798
2.1984-2.2694	0.174863852358	220	0.141278524017	4251	X-RAY DIFFRACTION	99.8882931189
2.2694-2.3505	0.218886616169	224	0.153216545684	4280	X-RAY DIFFRACTION	99.9556147359
2.3505-2.4446	0.206010972399	234	0.151756049812	4312	X-RAY DIFFRACTION	99.8681898067
2.4446-2.5558	0.164086021858	228	0.150489480257	4294	X-RAY DIFFRACTION	100
2.5558-2.6906	0.170690132324	222	0.150804885538	4274	X-RAY DIFFRACTION	100
2.6906-2.8591	0.210459231225	224	0.152234354458	4288	X-RAY DIFFRACTION	99.9335548173
2.8591-3.0798	0.178283370116	217	0.155338817211	4254	X-RAY DIFFRACTION	99.9552872792
3.0798-3.3897	0.170016898475	225	0.148908869681	4323	X-RAY DIFFRACTION	100
3.3897-3.8799	0.139143617837	223	0.132361527685	4259	X-RAY DIFFRACTION	100
3.8799-4.8874	0.153876863248	224	0.118830828872	4274	X-RAY DIFFRACTION	99.9333481449
4.8874-45.50728515	0.170889120592	225	0.157779609026	4301	X-RAY DIFFRACTION	99.933760212

Refinement TLS params.

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

ID	L11 (°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)
1	1.37377254805	-0.0337151905724	0.160368988311	1.40357659413	-0.0234598958641	1.44781537354	-0.057670029142	0.148860916251	-0.0852419792321	-0.12383025321	0.0845284895191	0.0473158422638	0.0142666155984	0.0345780159894	-0.0294878630383	0.109173299061	0.0049182225495	-0.00355624421642	0.108306005545	-0.0100226831707	0.0925546082709	-17.6898312316	9.18744109089	-38.4669634833
2	7.34178258841	-1.33208039242	-0.0503800675747	1.80220327228	-0.0190465288977	1.29334593009	-0.0487628382023	0.26253124803	-0.780779701386	-0.106190703573	-0.00591432348408	0.035249246737	0.150120826076	0.0968079305581	0.0679641184042	0.12170012842	0.0146708170966	-0.028014939724	0.135098926839	-0.0317598180137	0.159969313297	-10.5251005169	-0.71959387942	-35.6728032081
3	2.77440486757	0.206543450864	1.16400492853	2.19979509343	0.107920224366	2.84734865129	0.000158357557801	0.271338923406	-0.0295161036667	-0.257537812716	-0.0620381969122	-0.201760272772	-0.0198840101653	0.403587679528	0.0430193097456	0.146675556321	0.00349817335397	0.0268870837689	0.216236769576	-0.0350467714272	0.148038416144	-3.57492707759	6.8174758146	-40.9746737237
4	1.15454710701	-0.112487286826	-0.0313827770736	0.956387555975	0.174525516595	1.16186910215	-0.0191527684148	-0.14767855222	-0.0456478886927	0.144404392589	0.060211260534	-0.00309998838367	0.0621214676359	-0.0243561665874	-0.0661107878249	0.10963974214	-0.00310138211749	-0.00931579386058	0.106948446334	0.00860720866285	0.112124509534	-16.6590678796	6.34054488356	-22.629831915
5	4.75311313451	-3.26085535553	-0.0215831057071	2.74464676799	-0.395845398926	0.348964193626	0.0138799824524	0.138159922739	-0.496780686214	-0.0355995894207	-0.00876776115769	0.186443883532	0.10350476229	0.0455482243095	0.0135654954508	0.123604563366	0.0125234673891	-0.0370370939626	0.158624469112	-0.0220887612765	0.183883246261	-12.4365283343	-1.02464628024	-30.1135770538
6	0.579202781803	0.309113541689	0.00890578046259	1.55104336748	-0.0234876597454	1.56126373986	-0.045512644327	0.06268342485	-0.0678554768626	-0.00913751782896	0.089145397234	0.248116201268	-0.0506254554401	-0.112149441093	-0.0340582408201	0.0896238305449	0.00896055498488	-0.00459542172394	0.0842042758432	0.0153848963799	0.105938002409	-22.4108735611	11.7829349096	-30.831751659
7	4.16752119911	-0.623324044426	0.750795206734	3.1875126597	-0.107839594592	3.4015622961	0.0106658167823	-0.105392710903	0.11743838859	0.0257621992651	0.0394114373316	-0.161472315985	-0.333237995499	0.1709476951	-0.0767776795025	0.194254529972	-0.0438220550021	0.0380663693125	0.0803607240703	-0.00814711549791	0.180796223446	-8.3681881414	37.2526932721	-24.5406651688
8	4.28131517484	-2.67053691466	-1.49593332289	4.57153813401	0.925114675573	2.48015213967	0.0955630538616	-0.146767674609	0.209059815376	-0.141453985298	0.0728202155866	0.0490992043734	-0.371675490218	-0.0537582068627	-0.133289623723	0.201795085043	-0.0142630382025	0.0255614019251	0.105402189575	-0.00465653403425	0.15882971279	-15.5890246653	37.5812069855	-25.2383085886
9	1.51172370167	0.21600907524	-0.0714777983557	1.74551336161	0.250791967518	0.944203039131	-0.0479892841065	-0.0975100989395	0.114057475086	-0.121112340212	0.0401780874286	0.293942861289	-0.121764082834	-0.09618515192	0.0101263694385	0.156607302076	0.0108291039381	-0.0202533401395	0.0978778820861	0.0168857529758	0.147889465119	-23.829407393	33.7939470638	-22.0152004751
10	4.65849930744	0.188751917406	-3.70783029699	0.965088102582	0.0333466646905	3.69310301802	0.230958260799	0.42967013744	0.528467195616	-0.369800517113	0.061943765305	-0.0354400153957	-0.404704568578	-0.260709118312	-0.225781953965	0.278813893616	0.0149365251775	0.0531409966342	0.131639997417	0.0281216551687	0.199656334972	-16.654941085	38.676333703	-35.1279376557
11	1.49684858992	-0.200412738536	0.321890318616	1.85963408507	0.524854929624	2.64965559204	0.0894323153506	-0.25354158044	0.406851305122	0.0733329352556	0.203967602268	-0.63396981336	-0.613867913693	0.789208664898	-0.206200656055	0.336814373215	-0.10282943203	0.0625568112698	0.24856879354	-0.0530838561213	0.323208011801	-2.87571532478	38.9624360357	-29.8015927587
12	1.02978057429	-0.257394627233	-0.289198508389	1.29834465163	0.41757718533	0.308363503336	0.0564362707698	0.180508728142	0.0819708640918	-0.306669804515	-0.0223906159309	0.0700906787338	-0.141169828102	-0.0847962050893	-0.0199948781196	0.180431524991	0.015957597708	-0.015594893817	0.127816440674	0.0130518749369	0.106649412986	-21.593455132	26.2101816443	-34.1879990193
13	1.03990417094	-0.278117930165	0.108580943661	1.89259543588	0.44792056646	1.40725847772	-0.0468133470696	-0.123897052008	0.0896113172425	0.0240195955322	0.0425196142951	0.121794792599	-0.0782427772599	-0.072461784522	-0.0255645661264	0.100677088055	0.00939500634898	-0.017713941571	0.0702926160352	0.00744824955636	0.093864420489	-22.3855368534	28.4017069336	-22.1001911199
14	3.34305885356	0.387602147453	-1.58039899178	1.98324989217	-0.307963026095	3.49715429809	0.0257917429994	-0.119281061611	-0.106328600841	0.223572455161	0.0274451196797	0.0194677954592	0.0445752989008	0.111455794914	-0.0317223237583	0.155139766366	0.0273496980648	-0.0450986734868	0.174082503606	0.00824962206397	0.131154875367	-3.99755059658	8.9603463753	-7.81414787234
15	1.94502483476	-0.0696476936163	0.0528168495485	1.04692380123	0.0551793953133	1.03237470766	-0.0480407881881	-0.234818099342	-0.0815033871687	0.0733246789581	0.0325617067949	0.026508387177	0.0359254624936	-0.043245156324	0.011443997238	0.108399462957	0.00768252356971	-0.021788669188	0.125839844516	0.00611607322557	0.0852550512666	-13.2638105698	11.2747344172	-9.46853936219
16	2.40502562057	0.113383568386	-0.666982047936	1.38121068162	-0.391676636752	1.49623263773	-0.0655379228053	-0.240953780212	0.126975810695	0.191705068333	0.0598718134984	-0.105308216877	0.0191860825984	0.183201726527	0.0111673410911	0.13757449668	0.00172885128113	-0.0469450933005	0.169146242338	-0.00913836035944	0.120770863959	-2.38848007423	16.9575164332	-4.94857533289
17	2.88958406043	0.339903152977	0.590484889746	0.0493323981805	0.0886172483074	3.60263089728	0.0830011072322	-0.0712704315608	-0.275177967378	0.124956242848	0.114484402894	-0.630846337055	0.185737251557	0.494456225513	-0.0935275376253	0.142657242345	0.00427060008472	-0.0901205662276	0.270685440705	-0.0182357029436	0.297339689562	7.52325089964	18.2449297586	-10.8630586712
18	1.53270741277	0.029221832902	0.310808877219	1.20633206605	-0.146129619827	1.07210464413	-0.058107738611	-0.211194702049	0.231870555536	0.162395841764	0.0232362971625	0.00728339091574	-0.201899397266	-0.0300320385894	0.0330890492462	0.133551732014	0.00946096764197	-0.00866482440781	0.140247964096	-0.032421621277	0.100620659842	-13.9584987141	25.1369396847	-9.19524056459
19	0.932663993665	-0.525035551899	0.0257314207381	1.00533535456	-0.132676632605	1.11319725525	-0.0333008623803	-0.174331289541	-0.0594176819635	-0.0127275834881	0.0188485957504	0.0915070187402	0.0419183883349	-0.0304791967655	0.0224800084136	0.102748894725	-0.00324175071203	-0.00186731406801	0.131310859086	0.00384936506421	0.0826728125641	-17.2587995273	13.1481928542	-12.8732244361

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 179 through 237 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 238 through 255 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 256 through 281 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 282 through 330 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 331 through 347 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 348 through 371 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 179 through 194 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 195 through 210 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 211 through 237 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 238 through 258 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 259 through 281 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 282 through 347 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 348 through 371 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 180 through 200 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 201 through 237 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 238 through 265 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 266 through 281 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 282 through 347 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 348 through 371 )

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