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

ID or keywords:

Entry

Database: PDB / ID: 9faf

Title

Human adenovirus type 36 fiber knob in complex with 4-O,5-N-diacetylneuraminic acid

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: 1.76 Å

Authors

Strebl, M. / Liaci, A.M. / 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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Download

PDBx/mmCIF format	9faf.cif.gz	294.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9faf.ent.gz	193.8 KB	Display	PDB format
PDBx/mmJSON format	9faf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	9faeC 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)	59.457, 99.164, 110.987
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

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Protein / Sugars , 2 types, 6 molecules ABC

#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-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

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Non-polymers , 4 types, 415 molecules

#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 24% 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: Feb 14, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.76→50 Å / Num. obs: 65546 / % possible obs: 99 % / Redundancy: 13.1 % / B_iso Wilson estimate: 24.0065372835 Å² / CC_1/2: 0.999 / Net I/σ(I): 14.5
Reflection shell	Resolution: 1.76→1.85 Å / Num. unique obs: 9952 / CC_1/2: 0.647 / % possible all: 94.1

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.76→48.4263923799 Å / SU ML: 0.190195470242 / Cross valid method: FREE R-VALUE / σ(F): 1.33955552843 / Phase error: 19.9681857606
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.183908792121	3276	4.99801666006 %
R_work	0.165045589782	62270	-
obs	0.166009324593	65546	99.0195634111 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.700902052 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→48.4263923799 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4292	0	103	411	4806

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00660197200403	4564
X-RAY DIFFRACTION	f_angle_d	0.893841370206	6230
X-RAY DIFFRACTION	f_chiral_restr	0.0568107577326	708
X-RAY DIFFRACTION	f_plane_restr	0.00543749128654	791
X-RAY DIFFRACTION	f_dihedral_angle_d	11.5714817844	2711

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 (%)
1.76-1.7825	0.461016706191	110	0.425981821586	2105	X-RAY DIFFRACTION	77.9655051038
1.7825-1.8104	0.270106564086	141	0.293636146076	2669	X-RAY DIFFRACTION	100
1.8104-1.8401	0.314893595407	143	0.269881379096	2720	X-RAY DIFFRACTION	99.9301919721
1.8401-1.8718	0.264294253454	142	0.243185320051	2698	X-RAY DIFFRACTION	100
1.8718-1.9058	0.268252085634	143	0.230085142679	2703	X-RAY DIFFRACTION	99.9297752809
1.9058-1.9425	0.27794424551	141	0.242646560219	2687	X-RAY DIFFRACTION	99.8235086481
1.9425-1.9821	0.225115337325	144	0.208730517392	2734	X-RAY DIFFRACTION	100
1.9821-2.0252	0.192215262948	140	0.177469298025	2671	X-RAY DIFFRACTION	99.9289015286
2.0252-2.0724	0.212765937206	141	0.181297647723	2705	X-RAY DIFFRACTION	99.8246229393
2.0724-2.1242	0.190901277314	143	0.172895676068	2726	X-RAY DIFFRACTION	99.9303378614
2.1242-2.1816	0.219371111464	142	0.163782337323	2699	X-RAY DIFFRACTION	100
2.1816-2.2458	0.196869010912	142	0.165206296859	2695	X-RAY DIFFRACTION	99.9647639183
2.2458-2.3183	0.171580693024	145	0.170663302398	2755	X-RAY DIFFRACTION	99.9655291279
2.3183-2.4012	0.190951762423	142	0.159826000638	2691	X-RAY DIFFRACTION	100
2.4012-2.4973	0.213379423101	144	0.160540425184	2740	X-RAY DIFFRACTION	100
2.4973-2.6109	0.194795049046	145	0.154278869238	2742	X-RAY DIFFRACTION	100
2.6109-2.7486	0.164957597333	143	0.157220699379	2717	X-RAY DIFFRACTION	100
2.7486-2.9208	0.16688976425	145	0.16359849613	2764	X-RAY DIFFRACTION	99.9656357388
2.9208-3.1462	0.177895269175	144	0.164343951724	2743	X-RAY DIFFRACTION	100
3.1462-3.4628	0.163447349142	146	0.154486024217	2771	X-RAY DIFFRACTION	100
3.4628-3.9637	0.169302959409	147	0.144547718775	2787	X-RAY DIFFRACTION	100
3.9637-4.993	0.147437735943	148	0.120803863224	2804	X-RAY DIFFRACTION	100
4.993-48.4263923799	0.151901557151	155	0.158710266093	2944	X-RAY DIFFRACTION	99.9355046759

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	5.29610289813	-1.6715179101	0.703027970578	2.19064008699	-0.572640282047	1.82023667517	0.0385865311918	0.329378033178	-0.0644821431648	-0.128633852362	-0.0254545941791	0.0541981190957	0.0247617214105	-0.109946224625	-0.0299671611232	0.247322501697	-0.033106106108	-0.011298051237	0.286407206775	-0.0619759634418	0.163641975721	-11.9932226214	5.63522419011	-30.9023922291
2	1.34828334656	-0.95202670056	-0.0895355763982	1.73389887708	0.81730095468	1.22194768549	0.00354573998483	0.096539277551	-0.0458527277061	-0.0227434402984	-0.0889863090736	0.132484808224	-0.0573385044851	-0.175412216193	0.084197405207	0.181589950208	-0.013707377196	-0.00511900994359	0.21533714156	-0.00957257748164	0.18552486818	-14.3856985515	6.9657363842	-21.6921699282
3	1.94626307421	-0.349080991052	-0.399628412593	1.8201770319	-1.02652993459	1.64838979156	-0.0224557064559	0.171934913074	-0.198946760595	-0.156134416268	0.0352040876199	0.114069817865	0.260976548664	-0.200976321482	-0.0139030596897	0.273255879547	-0.0286999283503	-0.0350667854512	0.255209891841	-0.0739204094871	0.226278780083	-13.2945792194	-4.27433032097	-31.6417456512
4	2.47343061005	-0.415431104925	1.26243205072	1.17718553991	1.57655175882	3.53172011409	0.0168284353637	0.481610446954	-0.135562344765	-0.278258434777	0.00739086232861	-0.13349832496	0.185199889791	0.661802043443	0.0582790296784	0.314421975059	0.0334141979045	-0.0108293961094	0.363862404783	-0.0504556117893	0.246946314888	-3.13341930756	-6.21561247145	-34.1122631076
5	1.24237888635	-0.61489642491	0.129942041669	1.45180821546	0.0945114553646	1.52344339028	0.00732696605668	-0.0162350660976	-0.279770417934	0.115991369686	-0.0306286744449	0.257351624679	0.243052495037	-0.239132946565	-0.0071172894325	0.210125522081	-0.0512995213365	0.0128411561476	0.222158759249	-0.00362232594106	0.230213625685	-15.1891409718	-2.01279141485	-13.58588624
6	3.49140212636	-0.539041868981	-0.933008381333	0.305220899499	0.354799452915	3.59230983397	-0.0353732404721	-0.0733292329109	0.188719201817	-0.0475113753286	0.0444012353431	-0.0624326966505	-0.444213080153	-0.137326020627	-0.0119641105642	0.259296847088	0.00497386447686	-0.00816579362872	0.210747749811	-0.0172012193367	0.224380294893	-16.3752470707	19.4622636865	-15.6945936543
7	3.11096269498	1.64891967487	0.84338897677	7.11626323777	-0.716052815014	2.08455203495	0.195742433224	0.0541257925558	-0.343769590886	-0.0290589050299	-0.217336347866	-0.149924125603	0.388612622914	0.0358119062276	0.00871525558232	0.231358647281	-0.00710972066091	0.0114995459943	0.204358556298	-0.0198885577239	0.217325720304	-5.53338053161	-5.5080964155	-16.9311812023
8	2.38700865051	0.46435796497	0.293212739771	6.22068324829	1.4018673123	1.85518474461	0.0117520835074	-0.0142622828007	-0.0198323169673	-0.0140412906639	0.0894875829977	-0.466045258996	0.041033872085	0.0818749005936	-0.118491898524	0.132191530788	-0.0169366249074	0.00805936121082	0.286284993105	0.00263165731296	0.242874346109	17.0308334122	13.6979997971	-9.10753927214
9	1.35494639132	0.0686637595416	-0.211267402206	1.46235864807	1.03409161169	2.256567749	-0.0267540796056	0.108549483237	0.082368384811	-0.0558042457304	0.108011718526	-0.122940009355	-0.113800186392	0.322090687262	-0.0930745482412	0.188206550662	-0.038388006217	-0.00427488787162	0.264794883644	-0.00757399351198	0.233804788076	11.9096355416	15.3332338969	-11.5781191657
10	3.0132337478	0.316606647254	3.07521914795	1.4552399883	0.178061376414	3.15337344418	0.0743929464852	0.621530407999	-0.464219945019	-0.349979950069	0.117342997279	-0.508836076541	0.175207918051	0.735782750709	-0.25397211902	0.242141521283	-0.0244353501442	0.0571368800543	0.5203610327	-0.110637619732	0.35047027466	20.0220694422	6.69910314388	-22.9205476066
11	1.84531634136	0.209236096934	-0.225371208171	0.933503994286	0.671300442568	1.70466634696	-0.014620221387	0.264216152123	0.128455900308	-0.194672198183	0.0148542883235	0.0272842705931	-0.299501287592	0.0686464586744	0.017979055067	0.2296818582	-0.0192490218582	-0.0113689462066	0.218671882033	0.0154797527663	0.20609303014	0.763250302791	16.4076799239	-17.5634091228
12	1.07667613992	0.584382950329	0.779073697261	1.74535654513	0.45484664056	2.76639489842	0.0436784842883	-0.0347154643851	0.055621637816	0.141384317104	0.0678003978074	-0.027258922141	0.107987526406	0.161632637806	-0.131849762271	0.131355282905	-0.022777161336	0.00407622666904	0.187399409522	0.00213148502686	0.205910507578	2.7781701938	14.2752884639	-5.64829203027
13	2.98468937444	0.0566098315404	-0.466865681837	3.08706168338	1.08107424489	7.39882435017	-0.0825595204736	-0.122736330588	-0.268517394806	0.148824551988	0.13973920067	0.0311901021975	0.740269773119	-0.0495675847318	-0.0828101586451	0.382458382275	0.0222102250145	-0.0296405514845	0.15819859249	0.0310460668269	0.311728432103	-3.15685531068	-15.3147409447	-4.86849507788
14	1.5841063553	-0.300441251895	-0.625075113127	0.954505208065	0.13767844153	2.30397805887	-0.0977533219679	-0.0816930366398	-0.113134249645	0.106929339558	0.0503425634718	-0.00831423451432	0.364831433886	0.0322254395495	0.0608621199033	0.275663290418	0.0190246824701	-0.0155749560448	0.17994524288	0.0163519835256	0.246674264156	-3.34782950549	-8.80633793061	-1.96933030265
15	2.29320595477	-0.781502766531	-0.912839474277	1.23049466362	0.328471696385	1.33695473357	-0.0594245335882	-0.276128300869	-0.271664499419	0.105571716865	0.0378046504709	-0.102703428499	0.298915025109	0.103617615732	0.0284890454311	0.329780172041	0.0225457535129	-0.0121387539832	0.221079813774	0.0706164218203	0.280961163124	-2.96570966855	-9.94840179918	5.05703412224
16	2.56700807514	-0.556488209429	-0.0372043121315	1.52776212168	-0.179767039248	1.63926372936	-0.00247790953222	-0.25764143199	-0.125001652626	0.147550266379	0.00555294039089	-0.220109046002	0.161664240548	0.267311644841	-0.00508917558992	0.244138914039	0.00580518189738	-0.0263010887511	0.249452759157	0.0162008726525	0.211347390381	4.33454385718	-1.15419455183	0.948924079267
17	2.55010661223	0.570773504824	-0.375660931906	0.819915067004	-0.395609739245	2.22386744962	-0.10774518879	0.117396945348	-0.226291200295	0.104248613032	0.0370378706533	0.047478855621	0.166642006606	-0.180008212073	0.0769199250256	0.23048675615	-0.019820583038	-0.0101841060287	0.139712703913	0.0156546491936	0.177296257045	-8.06547101385	-0.0433764641631	-0.670797128321

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 180 through 200 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 201 through 245 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 246 through 264 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 265 through 281 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 282 through 347 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 348 through 362 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 363 through 371 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 180 through 200 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 201 through 265 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 266 through 281 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 282 through 347 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 348 through 371 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 180 through 194 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 195 through 222 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 223 through 265 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 266 through 347 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 348 through 371 )

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Protein / Sugars , 2 types, 6 molecules ABC

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Non-polymers , 4 types, 415 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi