7BAG: C3b

C3b in complex with CP40. Determined by X-ray diffraction at 2.0 Å resolution. Released 12 Jan 2022.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 13,417
Mol. weight: 178.33 kDa
Ligands: CA, ACM, NH2
Released: 12 Jan 2022

Explore 7BAG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BAG contains 58 α-helices and 108 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: 19 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
β-strand	11-13	3	2
β-strand	18-25	8	1
β-strand	31-39	9	2
β-strand	46-54	9	2
β-strand	61-66	6	1
α-helix	68-70	3
β-strand	82-90	9	2
β-strand	93-102	10	2
β-strand	107-112	6	3
β-strand	116-117	2	4
β-strand	122-130	9	3
β-strand	136	1	3
β-strand	140-146	7	4
β-strand	152-159	8	4
β-strand	166-172	7	3
α-helix	173-174	2
β-strand	180-188	9	4
β-strand	196-202	7	4
β-strand	210-216	7	5
β-strand	221-222	2	6
β-strand	229-237	9	5
α-helix	241	1
β-strand	242	1	5
α-helix	243	1
β-strand	245-255	11	7
β-strand	258-261	4	7
α-helix	263-265	3
β-strand	267-271	5	7
β-strand	272	1	5
β-strand	275-280	6	5
α-helix	282-287	6
α-helix	294-297	4
β-strand	301-310	10	7
β-strand	316-325	10	7
β-strand	326-327	2	6
β-strand	332-334	3	8
β-strand	341-342	2	9
β-strand	348-355	8	8
α-helix	360	1
β-strand	361	1	8
α-helix	362-363	2
β-strand	366-369	4	10
β-strand	376-378	3	10
β-strand	384-389	6	8
β-strand	398-404	7	10
α-helix	411-413	3
β-strand	416-421	6	10
β-strand	422-423	2	9
α-helix	424-426	3
α-helix	427-429	3
β-strand	433-437	5	11
β-strand	448-456	9	11
α-helix	462-464	3
β-strand	467-474	8	12
β-strand	477-485	9	12
β-strand	492-498	7	11
α-helix	501-503	3
β-strand	506-516	11	12
β-strand	522-532	11	12
β-strand	541-545	5	13
β-strand	558-566	9	13
β-strand	570-577	8	14
α-helix	578-583	6
α-helix	591-600	10
β-strand	608	1	12
α-helix	613-619	7
β-strand	622-626	5	1
β-strand	631	1	1
α-helix	632-635	4
α-helix	640-641	2

Chain B: 39 helices, 54 β-strands

Element	Residues	Length	Sheet
α-helix	736-738	3
β-strand	742	1	15
β-strand	748-749	2	14
β-strand	753-755	3	14
α-helix	759-760	2
β-strand	764-772	9	13
β-strand	778-788	11	14
β-strand	792-795	4	14
α-helix	796-798	3
β-strand	799-803	5	14
β-strand	807-812	6	16
β-strand	816-818	3	15
β-strand	823-831	9	16
β-strand	838-844	7	15
α-helix	845-846	2
β-strand	850-851	2	17
β-strand	860-866	7	15
β-strand	870-878	9	16
β-strand	879-880	2	17
β-strand	884-894	11	15
β-strand	900-910	11	15
β-strand	914-925	12	18
β-strand	936-937	2	19
β-strand	940	1	20
α-helix	941-943	3
β-strand	948	1	18
α-helix	949	1
β-strand	955-963	9	18
β-strand	966	1	21
α-helix	970-974	5
α-helix	975-981	7
α-helix	991-1008	18
α-helix	1012-1015	4
α-helix	1019-1034	16
α-helix	1035-1037	3
β-strand	1038	1	22
β-strand	1044	1	22
α-helix	1051-1053	3
α-helix	1054-1066	13
α-helix	1075-1089	15
β-strand	1090	1	23
β-strand	1096	1	23
α-helix	1105-1111	7
α-helix	1117-1136	20
α-helix	1143-1157	15
α-helix	1158-1160	3
α-helix	1164-1176	13
α-helix	1182-1191	10
β-strand	1193	1	24
β-strand	1197	1	24
α-helix	1204-1220	17
α-helix	1227-1237	11
α-helix	1247-1263	17
β-strand	1267	1	21
β-strand	1275	1	19
α-helix	1285-1287	3
β-strand	1308	1	20
β-strand	1311-1312	2	19
β-strand	1317-1328	12	18
β-strand	1339-1347	9	25
β-strand	1361-1370	10	25
β-strand	1376	1	26
β-strand	1379-1384	6	27
α-helix	1385-1386	2
β-strand	1389-1391	3	25
α-helix	1393-1400	8
β-strand	1405-1406	2	27
α-helix	1409-1412	4
β-strand	1421-1426	6	27
β-strand	1429	1	26
β-strand	1435-1443	9	25
β-strand	1453-1459	7	27
β-strand	1466-1471	6	27
α-helix	1476-1478	3
α-helix	1479-1481	3
β-strand	1482-1485	4	28
β-strand	1488-1491	4	28
α-helix	1507-1514	8
β-strand	1519-1531	13	29
β-strand	1536-1548	13	29
α-helix	1554-1555	2
β-strand	1559-1565	7	29
α-helix	1566-1571	6
β-strand	1579-1585	7	29
α-helix	1586-1588	3
β-strand	1589-1590	2	29
α-helix	1593-1595	3
β-strand	1597-1599	3	29
β-strand	1605-1609	5	29
α-helix	1612-1614	3
α-helix	1618-1620	3
α-helix	1621-1632	12
α-helix	1633-1637	5

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	30
β-strand	12	1	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3	A	protein	645	Homo sapiens	P01024 (AlphaFold model)
Complement C3	B	protein	915	Homo sapiens	P01024 (AlphaFold model)
Compstatin CP40	C	protein	14	synthetic construct

Sequence of entity 1 (A), FASTA

>7BAG_1 Complement C3 (chains A)
SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNH
MGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPG
STVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMG
QWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYG
KKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGK
SLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGS
PAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQ
ALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLK
AGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGS
LVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEK
ADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQPAA

Sequence of entity 2 (B), FASTA

>7BAG_2 Complement C3 (chains B)
SNLDEDIIAEENIVSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKDSITTWEILAVS
MSDKKGICVADPFEVTVMQDFFIDLRLPYSVVRNEQVEIRAVLYNYRQNQELKVRVELLH
NPAFCSLATTKRRHQQTVTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKS
LKVVPEGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDTESETRILLQGTPVA
QMTEDAVDAERLKHLIVTPSGCGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALEL
IKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLI
LEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGS
ITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLY
NVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPD
HQELNLDVSLQLPSRSSKITHRIHWESASLLRSEETKENEGFTVTAEGKGQGTLSVVTMY
HAKAKDQLTCNKFDLKVTIKPAPETEKRPQDAKNTMILEICTRYRGDQDATMSILDISMM
TGFAPDTDDLKQLANGVDRYISKYELDKAFSDRNTLIIYLDKVSHSEDDCLAFKVHQYFN
VELIQPGAVKVYAYYNLEESCTRFYHPEKEDGKLNKLCRDELCRCAEENCFIQKSDDKVT
LEERLDKACEPGVDYVYKTRLVKVQLSNDFDEYIMAIEQTIKSGSDEVQVGQQRTFISPI
KCREALKLEEKKHYLMWGLSSDFWGEKPNLSYIIGKDTWVEHWPEEDECQDEENQKQCQD
LGAFTESMVVFGCPN

Sequence of entity 3 (C), FASTA

>7BAG_3 Compstatin CP40 (chains C)
YICVWQDWGAHRCI

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
ACM	Acetamide	C2 H5 N O	1
NH2	Amino group	H2 N	1

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

Primary citation

Insight into mode-of-action and structural determinants of the compstatin family of clinical complement inhibitors. Lamers, C., Xue, X., Smiesko, M. et al. Nat Commun (2022) 13:5519-5519. DOI 10.1038/s41467-022-33003-7 · 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
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
4ZH1 2.24 Å, Complement factor H in complex with the GM1 glycan

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