3D5O: Serum amyloid P-component

Structural recognition and functional activation of FcrR by innate pentraxins. Determined by X-ray diffraction at 2.8 Å resolution. Released 11 Nov 2008.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,655
Mol. weight: 139.22 kDa
Ligands: NAG
Released: 11 Nov 2008

Explore 3D5O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D5O contains 21 α-helices and 127 β-strands across 6 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: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	7-11	5	2
β-strand	19-22	4	3
β-strand	30	1	4
β-strand	32-40	9	2
β-strand	47-53	7	3
β-strand	61-67	7	3
β-strand	70-75	6	3
β-strand	78-83	6	3
β-strand	92-99	8	2
β-strand	104-109	6	2
β-strand	112-113	2	2
β-strand	117-118	2	2
β-strand	125	1	4
β-strand	130-133	4	3
α-helix	146-148	3
β-strand	152-160	9	2
α-helix	166-173	8
β-strand	183-184	2	2
β-strand	188	1	1
β-strand	190-193	4	3
β-strand	197-200	4	2

Chain B: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	7-11	5	6
β-strand	19-22	4	7
α-helix	29	1
β-strand	30	1	8
β-strand	32-40	9	6
β-strand	47-53	7	7
β-strand	61-67	7	7
β-strand	70-75	6	7
β-strand	78-83	6	7
β-strand	92-99	8	6
β-strand	104-109	6	6
β-strand	112-113	2	6
α-helix	114-116	3
β-strand	117-118	2	6
β-strand	125	1	8
β-strand	130-133	4	7
β-strand	152-160	9	6
α-helix	166-173	8
α-helix	177-179	3
β-strand	183	1	6
β-strand	184	1	9
β-strand	187	1	9
β-strand	188	1	5
β-strand	190-193	4	7
β-strand	197-200	4	6

Chain C: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	10
β-strand	7-10	4	11
β-strand	19-22	4	12
α-helix	29	1
β-strand	30	1	13
β-strand	33-41	9	11
β-strand	47-54	8	12
β-strand	61-67	7	12
β-strand	70-75	6	12
β-strand	79-83	5	12
β-strand	92-98	7	11
β-strand	104-109	6	11
β-strand	112-113	2	11
β-strand	117-118	2	11
β-strand	125	1	13
β-strand	129-133	5	12
α-helix	146-148	3
β-strand	152-160	9	11
α-helix	166-174	9
α-helix	177-179	3
β-strand	183-184	2	11
α-helix	185-187	3
β-strand	188	1	10
β-strand	190-193	4	12
β-strand	197-200	4	11

Chain D: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	14
β-strand	7-11	5	15
β-strand	19-22	4	16
β-strand	30	1	17
β-strand	32-40	9	15
β-strand	47-53	7	16
β-strand	61-67	7	16
β-strand	70-75	6	16
β-strand	81-83	3	16
β-strand	92-99	8	15
β-strand	104-109	6	15
β-strand	112-113	2	15
β-strand	117-118	2	15
β-strand	125	1	17
β-strand	130-133	4	16
α-helix	146-148	3
β-strand	152-160	9	15
α-helix	166-173	8
β-strand	183-184	2	15
β-strand	188	1	14
β-strand	190-193	4	16
β-strand	197-200	4	15

Chain E: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	18
β-strand	19-22	4	19
β-strand	30	1	20
β-strand	32-40	9	18
β-strand	47-53	7	19
β-strand	61-65	5	19
β-strand	70-75	6	19
β-strand	78-83	6	19
β-strand	92-99	8	18
β-strand	104-109	6	18
β-strand	112-113	2	18
β-strand	117-118	2	18
β-strand	125	1	20
β-strand	130-133	4	19
α-helix	146-148	3
β-strand	152-160	9	18
α-helix	163-165	3
α-helix	166-172	7
β-strand	183-184	2	18
β-strand	187	1	18
β-strand	190-193	4	19
β-strand	197-200	4	18

Chain F: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4	1	21
α-helix	5	1
β-strand	6-10	5	22
β-strand	15-17	3	23
β-strand	21-27	7	22
β-strand	37-41	5	24
β-strand	44-45	2	24
β-strand	53-57	5	22
α-helix	60-62	3
β-strand	64-70	7	24
β-strand	74	1	21
β-strand	79-81	3	24
β-strand	82-84	3	23
β-strand	88-90	3	25
β-strand	96-98	3	26
β-strand	103-106	4	27
β-strand	107-109	3	25
α-helix	110-112	3
β-strand	116-117	2	28
β-strand	118	1	29
β-strand	119-121	3	28
β-strand	126	1	28
β-strand	130	1	29
β-strand	135-138	4	27
β-strand	147-149	3	30
β-strand	150-154	5	28
β-strand	161	1	28
α-helix	162-164	3
β-strand	165-167	3	30
β-strand	168-170	3	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serum amyloid P-component	A, B, C, D, E	protein	204	Homo sapiens	P02743 (AlphaFold model)
Low affinity immunoglobulin gamma Fc region receptor II-a	F	protein	177	Homo sapiens	P12318 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>3D5O_1 Serum amyloid P-component (chains A, B, C, D, E)
HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNE
LLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLR
QGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPA
NILDWQALNYEIRGYVIIKPLVWV

Sequence of entity 2 (F), FASTA

>3D5O_2 Low affinity immunoglobulin gamma Fc region receptor II-a (chains F)
APPKAVLKLEPPWINVLQEDSVTLTCQGARSPESDSIQWFHNGNLIPTHTQPSYRFKANN
NDSGEYTCQTGQTSLSDPVHLTVLSEWLVLQTPHLEFQEGETIMLRCHSWKDKPLVKVTF
FQNGKSQKFSRLDPTFSIPQANHSHSGDYHCTGNIGYTLFSSKPVTITVQVHHHHHH

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 (GOL, SO4) are not listed.

Primary citation

Structural recognition and functional activation of FcgammaR by innate pentraxins. Lu, J., Marnell, L.L., Marjon, K.D. et al. Nature (2008) 456:989-992. DOI 10.1038/nature07468 · PubMed

Other PDB entries of the same protein (UniProt P02743 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4AVS 1.4 Å, Structure of N-Acetyl-L-Proline bound to Serum Amyloid P Component
3KQR 1.5 Å, The structure of serum amyloid p component bound to phosphoethanolamine
4AYU 1.5 Å, Structure of N-Acetyl-D-Proline bound to serum amyloid P component
4AVV 1.6 Å, Structure of CPHPC bound to Serum Amyloid P Component
2W08 1.7 Å, The structure of serum amyloid P component bound to 0-phospho- threonine
1SAC 2.0 Å, The structure of pentameric human serum amyloid P component
2A3Y 2.0 Å, Pentameric crystal structure of human serum amyloid P-component bound to…
1GYK 2.2 Å, Serum Amyloid P Component co-crystallised with MOBDG at neutral pH
2A3W 2.2 Å, Decameric structure of human serum amyloid P-component bound to…
1LGN 2.8 Å, Decameric damp complex of human serum amyloid P component
2A3X 3.0 Å, Decameric crystal structure of human serum amyloid P-component bound to…
4AVT 3.2 Å, Structure of CPHPC bound to Serum Amyloid P Component

Browse structure collections

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