PDB-8ofv: Human adenovirus type 53 fiber-knob protein complexed with sialic acid

ID or keywords:

Entry

Database: PDB / ID: 8ofv

Title

Human adenovirus type 53 fiber-knob protein complexed with sialic acid

Components

Fiber protein

Fibrous protein

Keywords

VIRAL PROTEIN /

Adenovirus / Fiber knob / Ad25

Function / homology

Function and homology information

viral capsid /

cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function

Biological species

Human adenovirus 53

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.77 Å

Authors

Rizkallah, P.J. / Parker, A.L. / Mundy, R.M. / Baker, A.T.

Funding support

United Kingdom, 2items

Citation

Journal: Npj Viruses / Year: 2023
Title: Broad sialic acid usage amongst species D human adenovirus.
Authors: Mundy, R.M. / Baker, A.T. / Bates, E.A. / Cunliffe, T.G. / Teijeira-Crespo, A. / Moses, E. / Rizkallah, P.J. / Parker, A.L.

History

Deposition	Mar 16, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 20, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.title
Revision 1.2	May 8, 2024	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ofv.cif.gz	919.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8ofv.ent.gz	767.1 KB	Display	PDB format
PDBx/mmJSON format	8ofv.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/of/8ofv ftp://data.pdbj.org/pub/pdb/validation_reports/of/8ofv	HTTPS FTP

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Related structure data

Related structure data	8ofpC 8ofqC 8ofrC 8ofsC 8oftC 8ofuC 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 (6) #113 - May 2009 Influenza Neuraminidase similarity (1)

Deposited unit

A: Fiber protein

B: Fiber protein

C: Fiber protein

D: Fiber protein

E: Fiber protein

F: Fiber protein

G: Fiber protein

H: Fiber protein

I: Fiber protein

J: Fiber protein

K: Fiber protein

L: Fiber protein

hetero molecules

261 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fiber protein

B: Fiber protein

C: Fiber protein

hetero molecules

defined by software
Evidence: homology
65.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Fiber protein

E: Fiber protein

F: Fiber protein

hetero molecules

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

3

G: Fiber protein

H: Fiber protein

I: Fiber protein

hetero molecules

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

4

J: Fiber protein

K: Fiber protein

L: Fiber protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.555, 60.406, 243.686
Angle α, β, γ (deg.)	90.00, 99.88, 90.00
Int Tables number	3
Space group name H-M	P121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein	Fiber protein / Fibrous protein Mass: 21325.182 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus 53 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: E5RWD1

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Sugars , 2 types, 2 molecules

#5: Sugar

ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID /

N-Acetylneuraminic acid

Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₉NO₉ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DNeup5Acb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-neuraminic acid	COMMON NAME	GMML 1.0
b-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#6: Sugar

ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID /

Sialic acid

Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₉NO₉

Identifier	Type	Program
DNeup5Aca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-neuraminic acid	COMMON NAME	GMML 1.0
a-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 1582 molecules

#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Diethylene glycol diethyl ether Mass: 162.227 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₈H₁₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1542 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.65 Å³/Da / Density % sol: 53.6 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M PCTP buffer, 25 % w/v PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91188 Å / Relative weight: 1
Reflection	Resolution: 1.77→92.17 Å / Num. obs: 258349 / % possible obs: 98.7 % / Redundancy: 3.8 % / B_iso Wilson estimate: 17.4 Å² / CC_1/2: 0.685 / R_merge(I) obs: 0.168 / R_pim(I) all: 0.097 / R_rim(I) all: 0.195 / Net I/σ(I): 6
Reflection shell	Resolution: 1.77→1.8 Å / Redundancy: 3.9 % / R_merge(I) obs: 1.707 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 12686 / CC_1/2: 0.327 / R_pim(I) all: 0.966 / R_rim(I) all: 1.967 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS		data scaling
xia2		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.77→92.17 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.941 / SU B: 9.269 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22826	12949	5 %	RANDOM
R_work	0.20838	-	-	-
obs	0.20937	245379	98.67 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 27.311 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.3 Å²	0 Å²	-0.7 Å²
2-	-	0.62 Å²	-0 Å²
3-	-	-	-0.64 Å²

Refinement step

Cycle: 1 / Resolution: 1.77→92.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17596	0	333	1542	19471

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	18741
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	17827
X-RAY DIFFRACTION	r_angle_refined_deg	1.537	1.656	25383
X-RAY DIFFRACTION	r_angle_other_deg	1.321	1.58	41186
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.946	5	2295
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.565	24.078	841
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.65	15	3208
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.865	15	51
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	2541
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	22696
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	4302
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.687	0.68	9084
X-RAY DIFFRACTION	r_mcbond_other	0.687	0.68	9083
X-RAY DIFFRACTION	r_mcangle_it	1.268	1.013	11411
X-RAY DIFFRACTION	r_mcangle_other	1.268	1.013	11412
X-RAY DIFFRACTION	r_scbond_it	0.739	0.825	9656
X-RAY DIFFRACTION	r_scbond_other	0.739	0.825	9657
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.134	1.151	13973
X-RAY DIFFRACTION	r_long_range_B_refined	7.067	9.351	21431
X-RAY DIFFRACTION	r_long_range_B_other	7.018	8.697	21064
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	6165	0.1
1	2	B	6165	0.1
2	1	A	6127	0.09
2	2	C	6127	0.09
3	1	A	6276	0.08
3	2	D	6276	0.08
4	1	A	6140	0.1
4	2	E	6140	0.1
5	1	A	5737	0.11
5	2	F	5737	0.11
6	1	A	5961	0.09
6	2	G	5961	0.09
7	1	A	6258	0.08
7	2	H	6258	0.08
8	1	A	6121	0.1
8	2	I	6121	0.1
9	1	A	6401	0.07
9	2	J	6401	0.07
10	1	A	6189	0.09
10	2	K	6189	0.09
11	1	A	5706	0.11
11	2	L	5706	0.11
12	1	B	6322	0.09
12	2	C	6322	0.09
13	1	B	6260	0.1
13	2	D	6260	0.1
14	1	B	6525	0.07
14	2	E	6525	0.07
15	1	B	5756	0.11
15	2	F	5756	0.11
16	1	B	5881	0.1
16	2	G	5881	0.1
17	1	B	6387	0.08
17	2	H	6387	0.08
18	1	B	6448	0.08
18	2	I	6448	0.08
19	1	B	6163	0.1
19	2	J	6163	0.1
20	1	B	6450	0.06
20	2	K	6450	0.06
21	1	B	5687	0.11
21	2	L	5687	0.11
22	1	C	6264	0.09
22	2	D	6264	0.09
23	1	C	6323	0.09
23	2	E	6323	0.09
24	1	C	5819	0.09
24	2	F	5819	0.09
25	1	C	5901	0.1
25	2	G	5901	0.1
26	1	C	6390	0.08
26	2	H	6390	0.08
27	1	C	6322	0.08
27	2	I	6322	0.08
28	1	C	6140	0.09
28	2	J	6140	0.09
29	1	C	6337	0.07
29	2	K	6337	0.07
30	1	C	5731	0.09
30	2	L	5731	0.09
31	1	D	6141	0.09
31	2	E	6141	0.09
32	1	D	5666	0.1
32	2	F	5666	0.1
33	1	D	5834	0.1
33	2	G	5834	0.1
34	1	D	6230	0.08
34	2	H	6230	0.08
35	1	D	6106	0.09
35	2	I	6106	0.09
36	1	D	6164	0.08
36	2	J	6164	0.08
37	1	D	6222	0.08
37	2	K	6222	0.08
38	1	D	5566	0.11
38	2	L	5566	0.11
39	1	E	5691	0.11
39	2	F	5691	0.11
40	1	E	5824	0.1
40	2	G	5824	0.1
41	1	E	6319	0.08
41	2	H	6319	0.08
42	1	E	6451	0.06
42	2	I	6451	0.06
43	1	E	6084	0.1
43	2	J	6084	0.1
44	1	E	6382	0.06
44	2	K	6382	0.06
45	1	E	5614	0.11
45	2	L	5614	0.11
46	1	F	5785	0.09
46	2	G	5785	0.09
47	1	F	5767	0.1
47	2	H	5767	0.1
48	1	F	5697	0.11
48	2	I	5697	0.11
49	1	F	5756	0.1
49	2	J	5756	0.1
50	1	F	5762	0.1
50	2	K	5762	0.1
51	1	F	5716	0.09
51	2	L	5716	0.09
52	1	G	5854	0.1
52	2	H	5854	0.1
53	1	G	5762	0.11
53	2	I	5762	0.11
54	1	G	5902	0.09
54	2	J	5902	0.09
55	1	G	5824	0.1
55	2	K	5824	0.1
56	1	G	5686	0.11
56	2	L	5686	0.11
57	1	H	6345	0.08
57	2	I	6345	0.08
58	1	H	6242	0.08
58	2	J	6242	0.08
59	1	H	6373	0.07
59	2	K	6373	0.07
60	1	H	5698	0.1
60	2	L	5698	0.1
61	1	I	6226	0.09
61	2	J	6226	0.09
62	1	I	6477	0.06
62	2	K	6477	0.06
63	1	I	5737	0.1
63	2	L	5737	0.1
64	1	J	6143	0.09
64	2	K	6143	0.09
65	1	J	5690	0.11
65	2	L	5690	0.11
66	1	K	5646	0.1
66	2	L	5646	0.1

LS refinement shell

Resolution: 1.77→1.816 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	865	-
R_work	0.337	17767	-
obs	-	-	97.06 %

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	2.0488	0.5711	-0.1781	1.1074	0.1373	1.0977	0.0037	0.1634	-0.0827	-0.062	0.025	-0.0261	0.0445	0.1318	-0.0286	0.0331	0.0109	0.0769	0.0353	-0.0132	0.3144	15.977	18.127	14.255
2	1.0094	0.0651	-0.1401	1.5792	-0.1793	2.1626	0.0179	0.0077	0.1013	0.0145	-0.0319	0.0543	-0.0835	-0.1172	0.014	0.0146	0.0027	0.0595	0.008	-0.0141	0.3542	0.74	38.823	23.41
3	1.6985	-0.1449	0.5033	2.0828	0.0718	1.1628	-0.0088	-0.1365	0.0318	0.1778	-0.0173	-0.0601	0.0071	0.1293	0.0261	0.067	0.0091	0.0632	0.0762	-0.0232	0.2811	23.931	32.388	35.948
4	1.3986	-0.187	-0.3378	1.1621	0.3502	1.6645	0.0274	0.008	0.015	0.0695	-0.0108	-0.1436	-0.126	0.3488	-0.0166	0.2396	-0.0352	0.0935	0.1017	0.0076	0.324	44.917	46.229	85.308
5	1.1432	-0.1114	0.3525	1.6147	-0.0301	1.3666	0.0597	-0.032	-0.1092	0.003	-0.0549	0.0655	0.1163	-0.0519	-0.0048	0.2546	-0.0144	0.1164	0.0214	-0.0047	0.3038	27.572	25.619	89.175
6	0.7029	0.2546	-0.1235	2.4969	-0.5409	2.418	0.0266	0.1579	-0.0548	-0.0898	-0.018	0.0411	0.1595	0.0796	-0.0086	0.22	0.0366	0.0671	0.1159	-0.0431	0.3054	34.307	32.777	64.23
7	1.4361	-0.5407	-0.609	3.2759	0.0706	1.4711	-0.087	-0.2563	-0.0927	0.2889	0.0548	0.1734	0.0525	-0.2105	0.0322	0.1479	0.0213	0.1067	0.1627	0.0365	0.3197	-36.525	13.345	43.252
8	2.5685	0.3484	-0.1695	1.4289	-0.3676	1.0549	-0.0027	0.1606	0.0138	-0.096	0.0065	0.0991	-0.0542	-0.2009	-0.0037	0.0396	0.0168	0.0816	0.0496	-0.0052	0.3232	-34.486	26.938	19.591
9	1.1626	0.0012	0.2659	1.7665	-0.0235	1.6297	0.035	-0.0066	-0.1418	0.091	-0.0267	0.0285	0.0982	0.0826	-0.0083	0.0476	0.0047	0.1093	0.005	0.006	0.3528	-17.668	6.535	25.376
10	1.1907	-0.4518	-0.4688	1.1085	0.2032	1.9711	-0.0227	-0.1814	-0.0987	0.0816	0.0391	0.0862	0.0803	-0.118	-0.0164	0.2426	-0.0195	0.1073	0.0838	0.022	0.3507	4.676	37.148	116.282
11	1.2431	-0.053	0.1933	1.5208	0.3598	2.0589	0.0416	0.0584	0.0932	-0.0296	-0.0308	0.034	-0.1354	0.0298	-0.0108	0.2408	-0.0039	0.1226	0.0261	0.0117	0.3598	12.924	57.549	100.208
12	2.1311	0.4333	0.0071	3.0289	-0.2591	1.1118	0.0047	0.0382	0.1097	-0.141	0.0317	0.355	-0.0317	-0.3885	-0.0364	0.2527	0.035	0.0823	0.2492	0.0224	0.4523	-12.935	50.72	100.6
13	2.9332	-0.4666	-5.6957	0.4002	1.1337	11.2297	0.0793	-0.0635	-0.1272	-0.0002	-0.3284	0.0198	-0.2053	-0.112	0.2492	0.3647	-0.0021	-0.0331	0.3692	0.0026	0.3209	26.937	50.242	76.338
14	11.7029	-5.9418	-1.1273	11.3195	2.242	11.5199	0.4898	0.0941	0.0748	-0.1846	-0.3401	-0.0019	-0.0221	0.1113	-0.1497	0.3474	-0.0113	-0.0072	0.3108	0.009	0.3086	0.7	33.253	97.095

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	182 - 366
2	X-RAY DIFFRACTION	2	B	178 - 366
3	X-RAY DIFFRACTION	3	C	179 - 366
4	X-RAY DIFFRACTION	4	D	180 - 366
5	X-RAY DIFFRACTION	5	E	178 - 366
6	X-RAY DIFFRACTION	6	F	183 - 366
7	X-RAY DIFFRACTION	7	G	183 - 366
8	X-RAY DIFFRACTION	8	H	179 - 366
9	X-RAY DIFFRACTION	9	I	178 - 366
10	X-RAY DIFFRACTION	10	J	182 - 366
11	X-RAY DIFFRACTION	11	K	180 - 366
12	X-RAY DIFFRACTION	12	L	183 - 366
13	X-RAY DIFFRACTION	13	F	404
14	X-RAY DIFFRACTION	14	L	404

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