3NMS: Staphylococcal Complement Inhibitor

Staphylococcal Complement Inhibitor (SCIN) in complex with Human Complement C3c. Determined by X-ray diffraction at 4.1 Å resolution. Released 4 Aug 2010.

Method: X-ray diffraction
Resolution: 4.1 Å
Organisms: Homo sapiens, Staphylococcus aureus
Chains: 4
Atoms: 9,561
Mol. weight: 144.84 kDa
Ligands: NAG
Released: 4 Aug 2010

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

Secondary structure: helices and β-sheets

3NMS contains 26 α-helices and 101 β-strands across 4 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, 58 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
β-strand	11-13	3	2
β-strand	17-25	9	1
β-strand	31-39	9	2
β-strand	47	1	2
β-strand	51-54	4	2
β-strand	61-67	7	1
β-strand	83-90	8	2
β-strand	93-102	10	2
β-strand	106-112	7	3
β-strand	116-117	2	4
β-strand	123-124	2	5
β-strand	125-131	7	3
β-strand	136	1	3
β-strand	140-146	7	6
β-strand	152-159	8	6
β-strand	166-167	2	3
β-strand	170-171	2	5
β-strand	183-188	6	6
β-strand	191-198	8	6
β-strand	201-202	2	4
α-helix	206-208	3
β-strand	210-216	7	7
β-strand	221-222	2	8
β-strand	229-237	9	7
β-strand	242	1	7
β-strand	245-255	11	9
β-strand	258-261	4	9
α-helix	263-265	3
β-strand	267-271	5	9
β-strand	272	1	7
β-strand	275-280	6	7
α-helix	282-289	8
α-helix	295-297	3
β-strand	301-310	10	9
β-strand	316-325	10	9
β-strand	326-327	2	8
β-strand	332-334	3	10
β-strand	341-342	2	11
β-strand	347-355	9	10
β-strand	361	1	10
β-strand	367-369	3	12
β-strand	377	1	12
β-strand	380	1	10
β-strand	384-390	7	10
α-helix	391-392	2
β-strand	398-404	7	12
β-strand	416-421	6	12
β-strand	422-423	2	11
α-helix	424	1
β-strand	433-438	6	13
β-strand	445	1	14
β-strand	447	1	14
β-strand	448-456	9	13
α-helix	459-462	4
β-strand	467-474	8	15
β-strand	477-485	9	15
β-strand	492-498	7	13
α-helix	501-503	3
β-strand	506-517	12	15
β-strand	521-532	12	15
β-strand	541-545	5	16
β-strand	558-566	9	16
β-strand	570-577	8	17
α-helix	580-582	3
α-helix	591-599	9
β-strand	608	1	15
α-helix	613-619	7
β-strand	623-626	4	1

Chain B: 1 helix, 22 β-strands

Element	Residues	Length	Sheet
β-strand	742	1	23
β-strand	748-749	2	17
β-strand	753-755	3	17
β-strand	761	1	16
β-strand	764-772	9	16
α-helix	773-774	2
β-strand	779-788	10	17
β-strand	792-794	3	17
β-strand	799-802	4	17
β-strand	807-812	6	24
β-strand	816-818	3	25
β-strand	823-825	3	26
β-strand	826-831	6	24
β-strand	838-844	7	23
β-strand	850	1	27
β-strand	860-866	7	23
β-strand	870-873	4	24
β-strand	876-878	3	26
β-strand	880	1	27
β-strand	884-885	2	25
β-strand	890-894	5	23
β-strand	900-903	4	23
β-strand	908-910	3	25

Chain C: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	1339-1347	9	18
β-strand	1362-1370	9	18
α-helix	1375	1
β-strand	1376	1	19
β-strand	1379-1384	6	20
β-strand	1391	1	18
α-helix	1393-1400	8
β-strand	1405-1406	2	20
α-helix	1409-1413	5
α-helix	1416-1418	3
β-strand	1421-1426	6	20
β-strand	1429	1	19
β-strand	1435	1	18
β-strand	1438-1441	4	18
β-strand	1454-1459	6	20
β-strand	1467-1470	4	20
β-strand	1482-1484	3	21
β-strand	1489-1491	3	21
α-helix	1507-1513	7
β-strand	1519-1529	11	22
β-strand	1536-1548	13	22
β-strand	1559-1565	7	22
β-strand	1579-1585	7	22
α-helix	1586-1588	3
β-strand	1589	1	22
β-strand	1597-1599	3	22
β-strand	1605-1609	5	22
α-helix	1612-1614	3
α-helix	1621-1632	12
α-helix	1633-1637	5

Chain M: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-24	18
α-helix	26-32	7
α-helix	38-57	20
α-helix	60-73	14
α-helix	78-82	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3	A	protein	645	Homo sapiens	P01024 (AlphaFold model)
Complement C3	C	protein	343	Homo sapiens	P01024 (AlphaFold model)
Staphylococcal complement inhibitor	M	protein	88	Staphylococcus aureus	Q931M7 (AlphaFold model)
Complement C3	B	protein	206	Homo sapiens	P01024 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3NMS_1 Complement C3 (chains A)
SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNH
MGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPG
STVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMG
QWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYG
KKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGK
SLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGS
PAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQ
ALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLK
AGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGS
LVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEK
ADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQPAA

Sequence of entity 2 (C), FASTA

>3NMS_2 Complement C3 (chains C)
SEETKENEGFTVTAEGKGQGTLSVVTMYHAKAKDQLTCNKFDLKVTIKPAPETEKRPQDA
KNTMILEICTRYRGDQDATMSILDISMMTGFAPDTDDLKQLANGVDRYISKYELDKAFSD
RNTLIIYLDKVSHSEDDCLAFKVHQYFNVELIQPGAVKVYAYYNLEESCTRFYHPEKEDG
KLNKLCRDELCRCAEENCFIQKSDDKVTLEERLDKACEPGVDYVYKTRLVKVQLSNDFDE
YIMAIEQTIKSGSDEVQVGQQRTFISPIKCREALKLEEKKHYLMWGLSSDFWGEKPNLSY
IIGKDTWVEHWPEEDECQDEENQKQCQDLGAFTESMVVFGCPN

Sequence of entity 3 (M), FASTA

>3NMS_3 Staphylococcal complement inhibitor (chains M)
GTSSTSLPTSNEYQNEKLANELKSLLDELNVNELATGSLNTYYKRTIKISGQKAMYALKS
KDFKKMSEAKYQLQKIYNEIDEALKSKY

Sequence of entity 4 (B), FASTA

>3NMS_4 Complement C3 (chains B)
SNLDEDIIAEENIVSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKDSITTWEILAVS
MSDKKGICVADPFEVTVMQDFFIDLRLPYSVVRNEQVEIRAVLYNYRQNQELKVRVELLH
NPAFCSLATTKRRHQQTVTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKS
LKVVPEGIRMNKTVAVRTLDPERLGR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Molecular Basis for Complement Recognition and Inhibition Determined by Crystallographic Studies of the Staphylococcal Complement Inhibitor (SCIN) Bound to C3c and C3b. Garcia, B.L., Ramyar, K.X., Tzekou, A. et al. J Mol Biol (2010) 402:17-29. DOI 10.1016/j.jmb.2010.07.029 · PubMed

Other PDB entries of the same protein (UniProt P01024 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WY7 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
2WY8 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
7UE9 1.75 Å, Structure of anti-C3d Fab(3d8b) in complex with C3d
1C3D 1.8 Å, X-ray crystal structure of C3D: a C3 fragment and ligand for complement receptor 2
6RMT 2.0 Å, Crystal structure of disulphide-linked human C3d dimer
7BAG 2.0 Å, C3b in complex with CP40
1GHQ 2.04 Å, CR2-C3D complex structure
3D5R 2.1 Å, Crystal Structure of Efb-C (N138A) / C3d Complex
3OXU 2.1 Å, Complement components factor H CCP19-20 and C3d in complex
4I6O 2.14 Å, Crystal structure of chemically synthesized human anaphylatoxin C3a
4ONT 2.15 Å, Ternary host recognition complex of complement factor H, C3d, and sialic acid
2GOX 2.2 Å, Crystal structure of Efb-C / C3d Complex

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