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Glycosciences.DB structure entry #231: M2 N-glycan linked to Asn

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Format: CarbBank LINUCS GlycoCT_xml


 a-D-Manp-(1-6)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn


<?xml version="1.0" encoding="UTF-8"?>
 <sugar version="1.0">
 <residues>
 <basetype id="1" anomer="b" superclass="hex" ringStart="1" ringEnd="5" name="b-dglc-HEX-1:5">
 <stemtype id="1" type="dglc" />
 </basetype>
 <substituent id="2" name="n-acetyl" />
 <basetype id="3" anomer="b" superclass="hex" ringStart="1" ringEnd="5" name="b-dglc-HEX-1:5">
 <stemtype id="1" type="dglc" />
 </basetype>
 <substituent id="4" name="n-acetyl" />
 <basetype id="5" anomer="b" superclass="hex" ringStart="1" ringEnd="5" name="b-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </basetype>
 <basetype id="6" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </basetype>
 </residues>
 <linkages>
 <connection id="1" parent="1" child="2">
 <linkage id="1" parentType="d" childType="n">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="2" parent="1" child="3">
 <linkage id="2" parentType="o" childType="d">
 <parent pos="4" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="3" parent="3" child="4">
 <linkage id="3" parentType="d" childType="n">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="4" parent="3" child="5">
 <linkage id="4" parentType="o" childType="d">
 <parent pos="4" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="5" parent="5" child="6">
 <linkage id="5" parentType="o" childType="d">
 <parent pos="6" />
 <child pos="1" />
 </linkage>
 </connection>
 </linkages>
 <aglyca>
 <historicalData>
 <entry id="0" name="ASN" toResidue="1">
 <linkage parentType="n" childType="x">
 <parent pos="4" />
 <child pos="1" />
 </linkage>
 </entry>
 </historicalData>
 </aglyca>
 </sugar>

SNFG-style Graphics

3D Structure Model

download coordinates

Corresponding entries: 2

1 - 2 of 2 entries with matching glycan part

Structure entry #22944:

a-D-Manp-(1-6)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc

no NMR spectra

no literature references

no Ref

no GlycoMaps

Taxons

Structure entry #23248:

a-D-Manp-(1-3/6)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc

no NMR spectra

literature references

no GlycoMaps

Taxons

General Structure Data

Chemical Formula:	C₃₂H₅₄N₄O₂₂		#C	#H	#O	#N
Molec. Weight:	846		32	54	22	4
# Atoms:	112
# Residues:	5
# Heavy Atoms:	58

Superclasses:

Hex
Hex	2
HexNAc	2

Residues:

Residue	Count
A-D-MANP	1
ASN	1
B-D-GLCPNAC	2
B-D-MANP	1

NMR Proton Chemical Shift Info

MHz	500
Temperature	300
Solvent	D2O
Residue	Linkage	Proton	PPM	JFrom	JTo	Hz	Note
Asn		HA	3.971			0
Asn		HB	2.851			0
Asn		HB'	2.931			0
b-D-GlcpNAc	4	H1	5.071			0
b-D-GlcpNAc	4	NAC	2.014			0
b-D-GlcpNAc	4,4	H1	4.618			0
b-D-GlcpNAc	4,4	NAC	2.076			0
b-D-Manp	4,4,4	H1	4.767			0
b-D-Manp	4,4,4	H2	4.080			0
a-D-Manp	6,4,4,4	H1	4.915			0
a-D-Manp	6,4,4,4	H2	3.968			0

PDB references: 218

1 - 5 of 218 PDB entries

PDB ID 7zlk: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124

Description:

Source: Human immunodeficiency virus 1, Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-09-21

Entry features 7 distinct glycan structures [37 instances].

PDB ID 7qqf: Crystal structure of unliganded MYORG

Description:

Source: Homo sapiens

Experimental method: X-RAY DIFFRACTION

Resolution: 2.43Å

Release date: 2022-08-31

Entry features 5 distinct glycan structures [21 instances].

PDB ID 7oih: Glycosylation in the crystal structure of neutrophil myeloperoxidase

Description:

Source: Homo sapiens

Experimental method: X-RAY DIFFRACTION

Resolution: 2.603Å

Release date: 2022-08-24

Entry features 13 distinct glycan structures [30 instances].

PDB ID 7ucf: Structure of the BG505 SOSIP.664 trimer in complex with neutralizing antibody Fab fragments 10-1074 and BG24

Description:

Source: Human immunodeficiency virus 1, HOMO SAPIENS

Experimental method: X-RAY DIFFRACTION

Resolution: 4Å

Release date: 2022-08-17

Entry features 13 distinct glycan structures [18 instances].

PDB ID 7fd2: Cryo-EM structure of an alphavirus, Getah virus

Description:

Source: Getah virus

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-08-10

Entry features 4 distinct glycan structures [16 instances].

Literature references: 22

1 - 5 of 22 literature references

Reference #21945

Ugonotti J; Kawahara R; Loke I; Zhu Y; Chatterjee S; Tjondro HC; Sumer-Bayraktar Z; Neelamegham S; Thaysen-Andersen M

N-acetyl-β-D-hexosaminidases mediate the generation of paucimannosidic proteins via a putative noncanonical truncation pathway in human neutrophils.

Published 2022 in Glycobiology, 32: 218-229

Reference contains 8 structures

Reference #21726

Tjondro HC; Ugonotti J; Kawahara R; Chatterjee S; Loke I; Chen S; Soltermann F; Hinneburg H; Parker BL; Venkatakrishnan V; Dieckmann R; Grant OC; Bylund J; Rodger A; Woods RJ; Karlsson-Bengtsson A; Struwe WB; Thaysen-Andersen M

Hyper-truncated Asn355- and Asn391-glycans modulate the activity of neutrophil granule myeloperoxidase.

Published 2021 in J Biol Chem, 296: 100144

Reference contains 20 structures

Reference #21760

Matthies I; Abrahams JL; Jensen P; Oliveira T; Kolarich D; Larsen MR

N-Glycosylation in isolated rat nerve terminals.

Published 2021 in Mol Omics, 17: 517-532

Reference contains 26 structures

Reference #20862

Loke I; Østergaard O; Heegaard NHH; Packer NH; Thaysen-Andersen M

Paucimannose-Rich N-glycosylation of Spatiotemporally Regulated Human Neutrophil Elastase Modulates Its Immune Functions.

Published 2017 in Mol. Cell Proteomics, 16: 1507-1527

Reference contains 8 structures

Reference #20861

Thaysen-Andersen M; Venkatakrishnan V; Loke I; Laurini C; Diestel S; Parker BL; Packer NH

Human neutrophils secrete bioactive paucimannosidic proteins from azurophilic granules into pathogen-infected sputum.

Published 2015 in J. Biol. Chem., 290: 8789-802

Reference contains 13 structures

Further literature references from PDB entries: 118

1 - 5 of 118 literature references from PDB entries

Reference #22422

Wang A; Zhou F; Liu C; Gao D; Qi R; Yin Y; Liu S; Gao Y; Fu L; Xia Y; Xu Y; Wang C; Liu Z

Structure of infective Getah virus at 2.8 Å resolution determined by cryo-electron microscopy.

Published 2022 in Cell Discov, 8: 12

Reference #22485

van Schooten J; Farokhi E; Schorcht A; van den Kerkhof TLGM; Gao H; van der Woude P; Burger JA; Meesters TGR; Bijl T; Ghalaiyini R; Turner HL; Dorning J; van Schaik BDC; van Kampen AHC; Labranche CC; Stanfield RL; Sok D; Montefiori DC; Burton DR; Seaman

Identification of IOMA-class neutralizing antibodies targeting the CD4-binding site on the HIV-1 envelope glycoprotein.

Published 2022 in Nat Commun, 13: 4515

Reference #21929

Gao N; Gai Y; Meng L; Wang C; Wang W; Li X; Gu T; Louder MK; Doria-Rose NA; Wiehe K; Nazzari AF; Olia AS; Gorman J; Rawi R; Wu W; Smith C; Khant H; de Val N; Yu B; Luo J; Niu H; Tsybovsky Y; Liao H; Kepler TB; Kwong PD; Mascola JR; Qin C; Zhou T; Yu X; G

Development of Neutralization Breadth against Diverse HIV-1 by Increasing Ab-Ag Interface on V2.

Published 2022 in Adv Sci (Weinh), : e2200063

Reference #22023

Wang Z; Dang HV; Amaya M; Xu Y; Yin R; Yan L; Hickey AC; Annand EJ; Horsburgh BA; Reid PA; Smith I; Eden JS; Xu K; Broder CC; Veesler D

Potent monoclonal antibody-mediated neutralization of a divergent Hendra virus variant.

Published 2022 in Proc Natl Acad Sci U S A, 119: e2122769119

Reference #21981

Altomare CG; Adelsberg DC; Carreno JM; Sapse IA; Amanat F; Ellebedy AH; Simon V; Krammer F; Bajic G

Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain.

Published 2022 in mBio, : e0358021

NCBI Taxonomy ID	Scientific Name
4615	Ananas comosus
9606	Homo sapiens

Consortium for Functional Glycomics (CFG):

carbNlink_20501_D000

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