6RV6: Properdin lacking TSR3 based on anomalous data

Structure of properdin lacking TSR3 based on anomalous data. Determined by X-ray diffraction at 3.51 Å resolution. Released 21 Aug 2019.

Method: X-ray diffraction
Resolution: 3.51 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,191
Mol. weight: 47.07 kDa
Ligands: MAN
Released: 21 Aug 2019

Explore 6RV6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RV6 contains 14 α-helices and 35 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: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	29-36	8	1
β-strand	43-52	10	1
α-helix	53-56	4
β-strand	63-65	3	1
β-strand	73-74	2	1
α-helix	77-78	2
β-strand	79-80	2	2
α-helix	82-89	8
β-strand	98-103	6	3
β-strand	104-105	2	2
β-strand	111	1	4
β-strand	115	1	4
α-helix	116	1
β-strand	120-125	6	3
β-strand	135	1	5
α-helix	141-148	8
β-strand	154-160	7	6
α-helix	167-168	2
β-strand	169	1	5
β-strand	179-185	7	6

Chain B: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	265-268	4
β-strand	275-281	7	7
β-strand	301-307	7	7
α-helix	311-313	3
β-strand	314	1	8
β-strand	317-318	2	9
α-helix	319-321	3
α-helix	323-326	4
β-strand	328	1	10
β-strand	336	1	10
β-strand	342-347	6	10
β-strand	350-351	2	9
β-strand	354	1	8
α-helix	357-360	4
β-strand	365-372	8	10
β-strand	377-379	3	11
β-strand	380-382	3	12
α-helix	383-388	6
β-strand	391	1	3
β-strand	392	1	13
β-strand	400-406	7	13
β-strand	407-409	3	12
β-strand	417-420	4	14
β-strand	425-428	4	14
β-strand	429-432	4	10
β-strand	436-438	3	11
β-strand	448-454	7	13
α-helix	458-460	3
α-helix	464-473	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Properdin	A	protein	170	Homo sapiens	P27918 (AlphaFold model)
Properdin	B	protein	221	Homo sapiens	P27918 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6RV6_1 Properdin (chains A)
DPVLCFTQYEESSGKCKGLLGGGVSVEDCCLNTAFAYQKRSGGLCQPCRSPRWSLWSTWA
PCSVTCSEGSQLRYRRCVGWNGQCSGKVAPGTLEWQLQACEDQQCCPEMGGWSGWGPWEP
CSVTCSKGTRTRRRACNHPAPKCGGHCPGQAQESEACDTQQVCPENLYFQ

Sequence of entity 2 (B), FASTA

>6RV6_2 Properdin (chains B)
GVAGGWGPWGPVSPCPVTCGLGQTMEQRTCNHPVPQHGGPFCAGDATRTHICNTAVPCPV
DGEWDSWGEWSPCIRRNMKSISCQEIPGQQSRGRTCRGRKFDGHRCAGQQQDIRHCYSIQ
HCPLKGSWSEWSTWGLCMPPCGPNPTRARQRLCTPLLPKYPPTVSMVEGQGEKNVTFWGR
PLPRCEELQGQKLVVEEKRPCLHVPACKDPEEEELENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	12

Primary citation

Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System. Pedersen, D.V., Gadeberg, T.A.F., Thomas, C. et al. Front Immunol (2019) 10:2007-2007. DOI 10.3389/fimmu.2019.02007 · 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)
6S0B 2.31 Å, Crystal Structure of Properdin in complex with the CTC domain of C3/C3b
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
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…

Browse structure collections

About this viewer

MolViewer shows 6RV6 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.