[wwPDB] Carbohydrate Remediation

An archival-level carbohydrate remediation project that led to the re-release of over 14,000 PDB structures in July 2020. This update includes diverse oligosaccharides: glycosylation; metabolites such as maltose, sucrose, cellulose fragments; glycosaminoglycans, such as fragments of heparin and heparan sulfate; epitope patterns such as A/B blood group antigens and the H-type or Lewis-type stems; and many artificial carbohydrates mimicking or countering natural products (see documentation).

Starting in 2017, this PDB remediation aimed to standardize the biochemical nomenclature of the carbohydrate components following the IUPAC-IUBMB recommendations established by the carbohydrate community (PDF), and to provide uniform representation of oligosaccharides to improve the identification and searchability of oligosaccharides modeled in the PDB structures. During the remediation planning, wwPDB consulted community users and the PDBx/mmCIF Working Group and made data files available on GitHub in early 2020 for community feedback. wwPDB has collaborated with Robert Woods at University of Georgia in US, researchers at The Noguchi Institute and Soka University in Japan, and Thomas Lutteke in Germany to generate uniform linear descriptors for the oligosaccharide sequences.

To achieve these community goals, each oligosaccharide is represented as a branched entity with complete biochemical description and each glycosidic linkage specified. The full representation of carbohydrates is provided in the mmCIF format file, but this is not possible in legacy PDB format files (as the format has been frozen since 2012).

Proper indexing is necessary for branched entity representation and for generation of linear descriptors, hence the ordering (numbering) starts at the reducing end (#1), where the glycosylation occurs, to the non-reducing end in ascending order. Unique chain IDs are assigned to branched entities (oligosaccharides) to avoid residue numbering overlapped with protein residues and to enable consistent numbering for every oligosaccharide. For example, in PDB ID 6WPS, there are 5 oligosaccharides associated with the same protein chain A, the consistent ordering and numbering can only be retained with unique chain ID for each oligosaccharide in both PDBx/mmCIF and PDB format files

For archival consistency, a single-monosaccharide is defined as a non-polymer and treated consistently with other non-polymer ligands in the PDB. A single-monosaccharide occurring at a glycosylation site has a unique chain ID in the PDBx/mmCIF file (_atom_site.label_asym_id) but not in the PDB format file.

Using PDB ID 6WPS as an example, the PDBx/mmCIF data item _atom_site.label_asym_id corresponds to the column #7 in the atom_site coordinates section has an asym ID ‘Y’ for the 1st instance of single-monosaccharide, NAG bound to ASN 61 of protein chain ‘A’. The ‘Y’ value is unique for this monosaccharide. The additional chain ID (_atom_site.auth_asym_id) in the PDBx/mmCIF file that mapped to the PDB format file for this NAG is chain ‘A’, which is consistently represented as any other non-polymer ligands associated with the protein chain A.

#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
...
HETATM 27655 C C1 . NAG Y 6 . ? 191.103 162.375 206.665 1.00 47.28 ? 1301 NAG A C1 1
HETATM 27656 C C2 . NAG Y 6 . ? 191.067 161.665 208.065 1.00 47.22 ? 1301 NAG A C2 1
HETATM 27657 C C3 . NAG Y 6 . ? 190.138 160.434 207.960 1.00 47.42 ? 1301 NAG A C3 1
HETATM 27658 C C4 . NAG Y 6 . ? 188.730 160.906 207.541 1.00 48.73 ? 1301 NAG A C4 1
HETATM 27659 C C5 . NAG Y 6 . ? 188.838 161.622 206.176 1.00 48.66 ? 1301 NAG A C5 1
HETATM 27660 C C6 . NAG Y 6 . ? 187.494 162.153 205.709 1.00 48.17 ? 1301 NAG A C6 1
HETATM 27661 C C7 . NAG Y 6 . ? 193.233 161.885 209.217 1.00 47.40 ? 1301 NAG A C7 1
HETATM 27662 C C8 . NAG Y 6 . ? 194.594 161.311 209.471 1.00 47.45 ? 1301 NAG A C8 1
HETATM 27663 N N2 . NAG Y 6 . ? 192.418 161.218 208.414 1.00 47.36 ? 1301 NAG A N2 1
HETATM 27664 O O3 . NAG Y 6 . ? 190.069 159.774 209.231 1.00 47.22 ? 1301 NAG A O3 1
HETATM 27665 O O4 . NAG Y 6 . ? 187.867 159.778 207.435 1.00 48.89 ? 1301 NAG A O4 1
HETATM 27666 O O5 . NAG Y 6 . ? 189.760 162.757 206.285 1.00 47.83 ? 1301 NAG A O5 1
HETATM 27667 O O6 . NAG Y 6 . ? 186.953 163.102 206.622 1.00 49.06 ? 1301 NAG A O6 1
HETATM 27668 O O7 . NAG Y 6 . ? 192.879 162.950 209.739 1.00 47.58 ? 1301 NAG A O7 1
...

Author-provided chain ID and residue numbering for oligosaccharides are retained in the PDBx/mmCIF file (_pdbx_branch_scheme.auth_mon_id and _pdbx_branch_scheme.auth_seq_num, respectively). Users can map how carbohydrates are described in the corresponding primary citation to the PDBx/mmCIF files using _pdbx_branch_scheme mapping category. wwPDB strongly encourages depositors to use the wwPDB-assigned chain ID and residue numbers in any publication material.

For example, in PDB entry 6WPS

loop_
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_mon_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.hetero
J 4 NAG 1 I NAG 1 A NAG 1310 n
J 4 NAG 2 I NAG 2 A NAG 1311 n
K 4 NAG 1 J NAG 1 A NAG 1312 n
K 4 NAG 2 J NAG 2 A NAG 1313 n
L 4 NAG 1 K NAG 1 A NAG 1315 n
L 4 NAG 2 K NAG 2 A NAG 1316 n
M 4 NAG 1 M NAG 1 A NAG 1317 n
M 4 NAG 2 M NAG 2 A NAG 1318 n
N 5 NAG 1 N NAG 1 A NAG 1321 n
N 5 NAG 2 N NAG 2 A NAG 1322 n
N 5 BMA 3 N BMA 3 A BMA 1323 n
N 5 MAN 4 N MAN 4 A MAN 1325 n
N 5 MAN 5 N MAN 5 A MAN 1324 n
N 5 FUC 6 N FUC 6 A FUC 1320 n
O 4 NAG 1 O NAG 1 B NAG 1310 n
O 4 NAG 2 O NAG 2 B NAG 1311 n
P 4 NAG 1 P NAG 1 B NAG 1312 n
P 4 NAG 2 P NAG 2 B NAG 1313 n
Q 4 NAG 1 Q NAG 1 B NAG 1315 n
Q 4 NAG 2 Q NAG 2 B NAG 1316 n
R 4 NAG 1 R NAG 1 B NAG 1317 n
R 4 NAG 2 R NAG 2 B NAG 1318 n
S 5 NAG 1 S NAG 1 B NAG 1321 n
S 5 NAG 2 S NAG 2 B NAG 1322 n
S 5 BMA 3 S BMA 3 B BMA 1323 n
S 5 MAN 4 S MAN 4 B MAN 1325 n
S 5 MAN 5 S MAN 5 B MAN 1324 n
S 5 FUC 6 S FUC 6 B FUC 1320 n
...

As some users pointed out, single NAG could be just a part of the glycan that the author chose to build, as most natural N-glycans must have stem of a common core of 5 monosaccharides or its fucosylated version, such as those modeled in the PDB ID 6WPS. However, the PDB is a 3D-atomic coordinate archive in which the model coordinates are built based on supporting experimental data. Therefore, carbohydrates are described as-is in the modeled structures without reference to missing components of the presumed oligosaccharide sequence. If the author only builds a monosaccharide, then this monosaccharide is described as a non-polymer ligand.

Glycosylation annotation has been provided to facilitate searches of all glycosylation sites. A total of 45,000 glycosylation sites have been annotated in _struct_conn.pdbx_role in over 7500 PDB structures to identify all glycosylation sites and the monosaccharides bound at such sites. The annotation specifies the glycosylation sites, the monosaccharide identity and chain IDs in either PDB format or mmCIF format. In PDB ID 6WPS, a user can search N-Glycosylation in ‘_struct_conn.pdbx_role’ and find 16 glycosylation sites between ASN and NAG at chain A alone.

In addition, a total of 1040 carbohydrate ligands were reviewed and their nomenclature has been standardized in the PDB to follow the 1996 IUPAC recommendations. The updates of monosaccharides in the Chemical Component Dictionary include chemical names, synonyms, atom labels, modification vs common sugars tags, chemical types (e.g., isomers), structure feature types (e.g., anomers), and symbol identifiers (e.g., IUPAC condensed symbols). The chemical names provided in PDBx/mmCIF data item _chem_comp.name have been updated uniformly to include stereo- and ring- specific systematic names as described in the IUPAC recommendations. Trivial or common names are annotated in the new PDBx/mmCIF category, _pdbx_chem_comp_synonyms, with one name per row. Both the IUPAC extended-form symbol as described in the section 2-Carb-38.3 of the 1996 recommendation and the condensed-form symbol in 2-Carb-38.4 are provided in the identifier of an PDBx/mmCIF data item _pdbx_chem_comp_identifier.identifier. Carbohydrate features such as isomer, ring size, anomer, and aldose/ketose classification as described in the PDBx/mmCIF category _pdbx_chem_comp_feature.

The wwPDB encourages the community to use PDB/mmCIF format files rather than the frozen legacy PDB file format. The legacy format cannot support large structures. Currently, PDB format-files are not available for large structures that have either more than 62 chains or 99,999 atoms. In addition, the legacy format cannot support ligand ID codes beyond 3-characters, which will be needed in the coming years.

The wwPDB is committed to improving data representation in the PDB archive. Please do not hesitate to contact us at info@wwpdb.org.

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