PDB-8pvs: Targeting extended blood antigens by Akkermansia muciniphila enzy...

ID or keywords:

Entry

Database: PDB / ID: 8pvs

Title

Targeting extended blood antigens by Akkermansia muciniphila enzymes unveils a missing link for generating universal donor blood

Components

Alpha-1,3-galactosidase B

Keywords

HYDROLASE / Alpha-galactosidase / Akkermansia muciniphila / Blood conversion / Beta-helix

Function / homology

Function and homology information

: / : / alpha-galactosidase / alpha-galactosidase activity
Similarity search - Function

Biological species

Akkermansia muciniphila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

Jensen, M. / Abou Hachem, M. / Morth, J.P.

Funding support

Denmark, 1items

Citation

Journal: Nat Microbiol / Year: 2024
Title: Akkermansia muciniphila exoglycosidases target extended blood group antigens to generate ABO-universal blood.
Authors: Jensen, M. / Stenfelt, L. / Ricci Hagman, J. / Pichler, M.J. / Weikum, J. / Nielsen, T.S. / Hult, A. / Morth, J.P. / Olsson, M.L. / Abou Hachem, M.

History

Deposition	Jul 18, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.year
Revision 1.2	May 15, 2024	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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	May 22, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pvs.cif.gz	708.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8pvs.ent.gz		Display	PDB format
PDBx/mmJSON format	8pvs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pvs_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8pvs_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8pvs_validation.xml.gz	58.3 KB	Display
Data in CIF	8pvs_validation.cif.gz	87.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pv/8pvs ftp://data.pdbj.org/pub/pdb/validation_reports/pv/8pvs	HTTPS FTP

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Related structure data

Related structure data	8pxtC 8pxuC 8pxvC 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

Deposited unit

A: Alpha-1,3-galactosidase B

B: Alpha-1,3-galactosidase B

hetero molecules

163 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Alpha-1,3-galactosidase B

hetero molecules

defined by author
Evidence: gel filtration
81.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Alpha-1,3-galactosidase B

hetero molecules

defined by author
81.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	118.527, 134.035, 215.346
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-911- HOH
2	1	A-1331- HOH
3	1	B-948- HOH

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein

Alpha-1,3-galactosidase B / Exo-alpha-galactosidase B

Mass: 80905.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Akkermansia muciniphila (bacteria) / Gene: glaB, Amuc_0480 / Production host:

Escherichia coli (E. coli)
References: UniProt: B2UNU8, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, alpha-galactosidase

#2: Sugar

ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 5 types, 1053 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1037 / 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: 2.64 Å³/Da / Density % sol: 53.46 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.9 Details: 8% PEG20.000, 8% PEG550MME, 0.02 M Tris (pH 8.9), 1.2 M NaFormate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.68→48.99 Å / Num. obs: 193688 / % possible obs: 99.89 % / Redundancy: 13.9 % / B_iso Wilson estimate: 28.64 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.168 / R_pim(I) all: 0.046 / R_rim(I) all: 0.174 / Net I/σ(I): 10.01
Reflection shell	Resolution: 1.68→1.74 Å / Mean I/σ(I) obs: 0.44 / Num. unique obs: 19152 / CC_1/2: 0.346 / CC star: 0.717 / % possible all: 99.29

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
PHENIX	1.19.2_4158	refinement
xia2		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.68→48.99 Å / SU ML: 0.2728 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1998	9478	4.9 %
R_work	0.1698	184106	-
obs	0.1713	193584	99.81 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.88 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→48.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11368	0	61	1037	12466

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0089	11675
X-RAY DIFFRACTION	f_angle_d	0.9373	15780
X-RAY DIFFRACTION	f_chiral_restr	0.0685	1720
X-RAY DIFFRACTION	f_plane_restr	0.0094	2072
X-RAY DIFFRACTION	f_dihedral_angle_d	12.1615	4303

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 (%)
1.68-1.7	0.4116	309	0.4028	5834	X-RAY DIFFRACTION	95.89
1.7-1.72	0.4139	316	0.3858	6146	X-RAY DIFFRACTION	99.68
1.72-1.74	0.3766	318	0.366	6045	X-RAY DIFFRACTION	99.89
1.74-1.76	0.3598	329	0.3475	6073	X-RAY DIFFRACTION	99.98
1.76-1.78	0.3349	337	0.325	6057	X-RAY DIFFRACTION	99.98
1.78-1.81	0.3194	305	0.305	6139	X-RAY DIFFRACTION	99.91
1.81-1.83	0.3347	308	0.2719	6064	X-RAY DIFFRACTION	99.91
1.83-1.86	0.2943	318	0.2541	6160	X-RAY DIFFRACTION	99.95
1.86-1.89	0.2594	306	0.2308	6087	X-RAY DIFFRACTION	99.97
1.89-1.92	0.2583	307	0.2218	6096	X-RAY DIFFRACTION	99.91
1.92-1.96	0.2336	337	0.2194	6102	X-RAY DIFFRACTION	99.95
1.96-1.99	0.2584	304	0.2188	6131	X-RAY DIFFRACTION	99.95
1.99-2.03	0.2454	281	0.1921	6159	X-RAY DIFFRACTION	99.95
2.03-2.07	0.2153	301	0.1765	6097	X-RAY DIFFRACTION	99.97
2.07-2.12	0.221	354	0.1678	6100	X-RAY DIFFRACTION	100
2.12-2.17	0.2008	319	0.1651	6108	X-RAY DIFFRACTION	99.97
2.17-2.22	0.2245	301	0.1581	6138	X-RAY DIFFRACTION	99.98
2.22-2.28	0.196	336	0.1532	6135	X-RAY DIFFRACTION	99.98
2.28-2.35	0.1798	297	0.151	6159	X-RAY DIFFRACTION	100
2.35-2.42	0.2115	308	0.1595	6135	X-RAY DIFFRACTION	100
2.42-2.51	0.1932	301	0.1574	6140	X-RAY DIFFRACTION	99.98
2.51-2.61	0.1987	333	0.1582	6135	X-RAY DIFFRACTION	100
2.61-2.73	0.1841	300	0.1588	6187	X-RAY DIFFRACTION	99.98
2.73-2.87	0.1981	321	0.1592	6162	X-RAY DIFFRACTION	100
2.87-3.05	0.2095	309	0.1636	6188	X-RAY DIFFRACTION	100
3.05-3.29	0.1939	324	0.1681	6177	X-RAY DIFFRACTION	100
3.29-3.62	0.1968	311	0.1601	6217	X-RAY DIFFRACTION	100
3.62-4.14	0.1765	308	0.1493	6226	X-RAY DIFFRACTION	100
4.14-5.22	0.1291	313	0.1197	6297	X-RAY DIFFRACTION	100
5.22-48.99	0.1795	367	0.1611	6412	X-RAY DIFFRACTION	99.63

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	0.534322942447	0.0667116208562	0.00888994833903	0.555650730523	-0.137312118984	0.476347808722	0.0320460256294	-0.0989020544923	-0.0545902748584	0.120540826195	-0.034369916801	-0.0232955418556	0.038897083579	0.0407797769297	-4.06750385201E-6	0.322690301389	-0.0718424708692	-0.00334510169479	0.284803897104	0.00426308708188	0.247528097367	-25.8494971594	-5.2354756738	-18.0440837945
2	0.772929528629	0.267162692893	0.23790386205	0.666913515138	-0.0751931046715	0.560999112135	0.0057028371118	-0.0586654032457	0.00863648633817	0.017322738506	0.0563320220826	0.113279879609	0.0760861968182	-0.120808112619	1.9764583955E-6	0.29818220049	-0.0688438471036	0.0052264638602	0.319394381338	0.0118950216389	0.293679618246	-45.182582245	-2.74495095749	-33.8111357648
3	0.558555234112	0.0676292034701	0.0290751098959	0.60932364215	0.34105454465	0.598810558052	-0.075330242417	0.0982726780722	0.338312053562	-0.118515735995	-0.0545691541052	0.211581445093	-0.167637887941	-0.136995706116	-1.91017457842E-6	0.335710966051	-0.0201234540239	-0.0754790982658	0.352422316083	0.0522791574457	0.539783208602	-41.1305952077	28.3602890758	-48.1366189383
4	0.55703944429	0.26244531656	0.0118040197977	0.180104385936	-0.0492917020599	0.517013455768	-0.0525715009291	0.0767375416157	0.0309546449147	-0.0654494552733	0.0605075958152	0.124376556901	0.151735342477	-0.111673249713	4.6530626907E-7	0.297274066051	-0.0770723024001	-0.0240941640925	0.307779133204	0.0249590309858	0.297706560401	-38.1457287502	2.33303478362	-47.5418877481
5	1.01315042736	-0.00511479463002	-0.051494869127	0.218641625579	-0.179320935113	0.481901786517	-0.05723697548	0.162417049028	0.00833730569897	-0.098655468573	0.0294558013924	-0.00451749908803	0.156417574915	0.058951792976	0.000119210863203	0.328432551003	-0.0579081371181	0.00971970603368	0.304453139688	0.00202498788463	0.244286619091	-20.6143027793	0.938224102414	-54.8691660821
6	0.451857288976	-0.466399797484	0.22832151191	1.04520596597	0.352020843441	0.739097534434	0.0203357275912	0.620626166382	0.249587770305	-0.316514326342	-0.0181441007612	-0.131711037429	0.0204625800381	0.0859173768626	0.144224141344	0.442410764486	-0.0880908749855	-0.00487843173313	0.596835266602	0.117549573663	0.254325211351	-23.8309235061	6.79711727992	-77.731135749
7	0.66104577608	0.23725274984	0.315410078424	0.674576802281	0.0413086955402	0.97155080241	-0.148717004297	0.162795841658	0.0758999906623	-0.193790846881	0.081724003412	0.0909295162742	-0.0767822145755	-0.0286017630656	-3.74715066067E-6	0.310361128994	-0.0605602233889	-0.0351015868935	0.276690247957	0.0306923696269	0.287200503694	-10.5821126749	40.8881344656	-37.5534490498
8	0.734837926728	0.338866883128	0.131281143037	0.637229344413	-0.272227713189	0.738683390952	-0.00269165472639	0.0404444536697	-0.0574276026646	-0.091359887745	0.0447992100126	0.00914279845058	0.117191950039	-0.0333126514858	-5.00693223027E-6	0.283930273385	-0.0310658346748	0.00556398627996	0.221042345583	-0.0257125417148	0.267320364028	-5.88820013001	21.9504622331	-21.9988957985
9	1.27391331519	0.310465484679	-0.488122083956	0.313473143282	0.19491469485	0.82944888821	-0.087311603389	-0.0925927085918	-0.129884969293	0.0261384548257	0.0351183756722	-0.0985247778225	0.111996023466	0.206679068041	-3.47556194973E-6	0.261247156686	0.0252691096609	-0.0097918039402	0.290713609844	0.00174868472883	0.340826428782	24.7606841217	29.8704663371	-7.63135211837
10	0.562165107225	-0.0331241673712	0.16815025622	0.568325378075	0.109088555534	0.610264305047	-0.00571649243586	-0.134107434743	0.0759043753173	0.00798999714421	-0.00248259524812	0.0361776222844	-0.00276990477684	-0.0467026072437	3.04656171739E-6	0.203928751345	-0.0156765919766	0.0101835637296	0.227556715317	-0.0309725847828	0.262557909341	-3.94794543473	41.755917343	-2.80682106389
11	0.390223725454	-0.141916022685	0.00123385526608	0.30395830843	-0.153564487323	0.57698621134	-0.13993480762	-0.762831663398	0.259639904713	0.399559793298	0.142820007589	-0.0692584081321	-0.0659679773687	0.0482755667165	0.00248768188522	0.408676349204	0.0104934026353	-0.0301222837377	0.534937587735	-0.119801247949	0.300637444665	1.34966580565	43.9099490921	22.1282354066

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 145 )	A	A	1 - 145	1 - 145
2	2	chain 'A' and (resid 146 through 267 )	A	A	146 - 267	146 - 267
3	3	chain 'A' and (resid 268 through 368 )	A	A	268 - 368	268 - 368
4	4	chain 'A' and (resid 369 through 455 )	A	A	369 - 455	369 - 455
5	5	chain 'A' and (resid 456 through 669 )	A	A	456 - 669	456 - 669
6	6	chain 'A' and (resid 670 through 731 )	A	A	670 - 731	670 - 731
7	7	chain 'B' and (resid 1 through 145 )	B	G	1 - 145	1 - 145
8	8	chain 'B' and (resid 146 through 267 )	B	G	146 - 267	146 - 267
9	9	chain 'B' and (resid 268 through 368 )	B	G	268 - 368	268 - 368
10	10	chain 'B' and (resid 369 through 669 )	B	G	369 - 669	369 - 669
11	11	chain 'B' and (resid 670 through 731 )	B	G	670 - 731	670 - 731

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Jul 12, 2017. Major update of PDB

-
Yorodumi