6S0B: Properdin

Crystal Structure of Properdin in complex with the CTC domain of C3/C3b. Determined by X-ray diffraction at 2.31 Å resolution. Released 4 Sept 2019.

Method: X-ray diffraction
Resolution: 2.31 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,645
Mol. weight: 56.21 kDa
Ligands: NAG, MAN
Released: 4 Sept 2019

Explore 6S0B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S0B contains 24 α-helices and 42 β-strands across 3 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: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	256	1	1
β-strand	264-265	2	2
β-strand	275-281	7	2
α-helix	288-289	2
β-strand	290	1	1
α-helix	293-296	4
β-strand	301-307	7	2
α-helix	310-313	4
β-strand	314	1	3
β-strand	317-318	2	4
α-helix	319-321	3
α-helix	323-326	4
β-strand	328	1	5
β-strand	342-347	6	5
β-strand	350-351	2	4
β-strand	354	1	3
α-helix	357-361	5
β-strand	365-372	8	5
β-strand	377-379	3	6
β-strand	380-382	3	7
α-helix	383	1
α-helix	385-388	4
β-strand	391	1	8
β-strand	392	1	9
β-strand	400-406	7	9
β-strand	407-409	3	7
β-strand	417-419	3	10
β-strand	426-428	3	10
β-strand	429-432	4	5
β-strand	436-438	3	6
α-helix	439-441	3
β-strand	442	1	11
β-strand	445	1	11
β-strand	448-454	7	9
α-helix	455	1
α-helix	458-460	3

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	30-37	8	12
β-strand	42-51	10	12
α-helix	53-56	4
β-strand	63-65	3	12
α-helix	71-72	2
β-strand	73-74	2	12
α-helix	77-78	2
β-strand	79-80	2	13
α-helix	81-88	8
β-strand	95-103	9	8
β-strand	104-105	2	13
β-strand	111	1	14
β-strand	115	1	14
α-helix	116	1
β-strand	120-128	9	8

Chain C: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1526-1528	3
α-helix	1529-1535	7
β-strand	1541-1551	11	15
β-strand	1559-1570	12	15
α-helix	1576-1577	2
β-strand	1581-1586	6	15
α-helix	1588-1590	3
α-helix	1591-1594	4
β-strand	1601-1607	7	15
α-helix	1608-1610	3
β-strand	1611	1	15
β-strand	1620-1621	2	15
β-strand	1627-1631	5	15
α-helix	1636-1638	3
α-helix	1643-1659	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Properdin	A	protein	225	Homo sapiens	P27918 (AlphaFold model)
Properdin	B	protein	110	Homo sapiens	P27918 (AlphaFold model)
Complement C3	C	protein	149	Homo sapiens	P01024 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6S0B_1 Properdin (chains A)
GSVAGGWGPWGPVSPCPVTCGLGQTMEQRTCNHPVPQHGGPFCAGDATRTHICNTAVPCP
VDGEWDSWGEWSPCIRRNMKSISCQEIPGQQSRGRTCRGRKFDGHRCAGQQQDIRHCYSI
QHCPLKGSWSEWSTWGLCMPPCGPNPTRARQRLCTPLLPKYPPTVSMVEGQGEKNVTFWG
RPLPRCEELQGQKLVVEEKRPCLHVPACKDPEEEELAAAHHHHHH

Sequence of entity 2 (B), FASTA

>6S0B_2 Properdin (chains B)
GSDPVLCFTQYEESSGKCKGLLGGGVSVEDCCLNTAFAYQKRSGGLCQPCRSPRWSLWST
WAPCSVTCSEGSQLRYRRCVGWNGQCSGKVAPGTLEWQLQACEDQQCAAA

Sequence of entity 3 (C), FASTA

>6S0B_3 Complement C3 (chains C)
GSNCFIQKSDDKVTLEERLDKACEPGVDYVYKTRLVKVQLSNDFDEYIMAIEQTIKSGSD
EVQVGQQRTFISPIKCREALKLEEKKHYLMWGLSSDFWGEKPNLSYIIGKDTWVEHWPEE
DECQDEENQKQCQDLGAFTESMVVFGCPN

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
MAN	alpha-D-mannopyranose	C6 H12 O6	8

Primary citation

Insights Into Enhanced Complement Activation by Structures of Properdin and Its Complex With the C-Terminal Domain of C3b. van den Bos, R.M., Pearce, N.M., Granneman, J. et al. Front Immunol (2019) 10:2097-2097. DOI 10.3389/fimmu.2019.02097 · PubMed

Other PDB entries of the same protein (UniProt P27918 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Q6R 1.9 Å, Structure of complement FP in complex with the TPP-3077 VHH
6S08 2.03 Å, Crystal Structure of Properdin (TSR domains N1 & 456)
6S0A 2.52 Å, Crystal Structure of Properdin (TSR domains N12 & 456)
9U62 2.7 Å, AP pathways C3 convertase C3bBbP and C3 complex
6RUS 2.8 Å, Structure of a functional properdin monomer
7B26 3.4 Å, CirpA1 in complex with pseudo-monomeric Properdin lacking TSR2-3
6SEJ 3.5 Å, Structure of a functional monomeric properdin lacking TSR3
6RV6 3.51 Å, Structure of properdin lacking TSR3 based on anomalous data
7NOZ 3.9 Å, Structure of the nanobody stablized properdin bound alternative pathway proconvertase…
6RUR 6.0 Å, Structure of the SCIN stabilized C3bBb convertase bound to properdin
6RUV 6.15 Å, Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the…
1W0R Solution structure of dimeric form of properdin by X-ray solution scattering and…

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