9DFT: G1 domain of human aggrecan

G1 domain of human aggrecan. Determined by X-ray diffraction at 3.5 Å resolution. Released 30 Apr 2025.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,758
Mol. weight: 75.62 kDa
Ligands: NAG
Released: 30 Apr 2025

Explore 9DFT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DFT contains 15 α-helices and 54 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	30-32	3	1
β-strand	38-42	5	2
β-strand	47-49	3	3
β-strand	52-54	3	1
β-strand	72-79	8	2
β-strand	82-90	9	2
β-strand	93-96	4	2
β-strand	104-105	2	3
β-strand	115	1	1
β-strand	118-120	3	3
α-helix	125-127	3
β-strand	129-137	9	2
β-strand	140-151	12	2
β-strand	153-157	5	4
β-strand	166	1	5
α-helix	168-177	10
β-strand	181-182	2	4
α-helix	183-184	2
α-helix	185-194	10
β-strand	202-203	2	4
β-strand	208-213	6	4
β-strand	229-235	7	4
β-strand	242	1	5
β-strand	243-248	6	4
β-strand	255-258	4	6
β-strand	264	1	7
α-helix	266-275	10
β-strand	279-280	2	6
α-helix	283-291	9
β-strand	300-301	2	6
β-strand	307-309	3	8
α-helix	331-333	3
β-strand	334-336	3	8
β-strand	344	1	7
β-strand	345-349	5	6

Chain B: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	30-32	3	9
β-strand	38-42	5	10
β-strand	47-49	3	11
β-strand	52-54	3	9
α-helix	68-71	4
β-strand	72-79	8	10
β-strand	82-90	9	10
β-strand	93-96	4	10
β-strand	104-105	2	11
β-strand	115	1	9
β-strand	118-120	3	11
β-strand	129-137	9	10
β-strand	140-151	12	10
β-strand	153-157	5	12
α-helix	168-177	10
β-strand	181-182	2	12
α-helix	183-184	2
α-helix	185-193	9
β-strand	202-204	3	12
β-strand	208-210	3	12
β-strand	243-248	6	12
β-strand	255	1	13
β-strand	264	1	14
α-helix	266-275	10
β-strand	279-280	2	13
α-helix	281-282	2
α-helix	283-291	9
β-strand	300-301	2	15
β-strand	307-311	5	15
β-strand	324-327	4	15
α-helix	337-339	3
β-strand	344	1	14
β-strand	345-346	2	15
β-strand	348-349	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aggrecan core protein	A, B	protein	335	Homo sapiens	P16112 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9DFT_1 Aggrecan core protein (chains A, B)
GPGSETSDHDNSLSVSIPQPSPLRVLLGTSLTIPCYFIDPMHPVTTAPSTAPLAPRIKWS
RVSKEKEVVLLVATEGRVRVNSAYQDKVSLPNYPAIPSDATLEVQSLRSNDSGVYRCEVM
HGIEDSEATLEVVVKGIVFHYRAISTRYTLDFDRAQRACLQNSAIIATPEQLQAAYEDGF
HQCDAGWLADQTVRYPIHTPREGCYGDKDEFPGVRTYGIRDTNETYDVYCFAEEMEGEVF
YATSPEKFTFQEAANECRRLGARLATTGQLYLAWQAGMDMCSAGWLADRSVRYPISKARP
NCGGNLLGVRTVYVHANQTGYPDPSSRYDAICYTG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Water and common crystallization additives (SO4) are not listed.

Primary citation

Aggrecan immobilizes to perineuronal nets through hyaluronan-dependent and hyaluronan-independent binding activities. Otsuka, M.Y., Essel, L.B., Sinha, A. et al. J Biol Chem (2025) 301:108525-108525. DOI 10.1016/j.jbc.2025.108525 · PubMed

Other PDB entries of the same protein (UniProt P16112 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4MD4 1.95 Å, Immune Receptor
9DFF 2.59 Å, G1 domain of human aggrecan bound to hyaluronan
7RDV 2.9 Å, TFH TCR bound to MHC Class II IAd presenting aggrecan epitope

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