3HRZ: Cobra Venom Factor

Cobra Venom Factor (CVF) in complex with human factor B. Determined by X-ray diffraction at 2.2 Å resolution. Released 7 Jul 2009.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Naja kaouthia, Homo sapiens
Chains: 4
Atoms: 15,938
Mol. weight: 227.04 kDa
Ligands: MG, NAG, PO4
Released: 7 Jul 2009

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

Secondary structure: helices and β-sheets

3HRZ contains 69 α-helices and 161 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: 17 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	10-12	3	2
β-strand	13	1	3
β-strand	17-18	2	4
β-strand	20-24	5	1
β-strand	30-39	10	2
β-strand	45-53	9	2
α-helix	55-57	3
β-strand	60-61	2	1
β-strand	64-65	2	4
β-strand	67	1	3
α-helix	69-71	3
β-strand	81-88	8	2
β-strand	91-100	10	2
β-strand	106-110	5	5
β-strand	114-115	2	6
β-strand	120-121	2	7
β-strand	123-127	5	5
β-strand	139-144	6	6
β-strand	150-156	7	6
β-strand	157	1	8
β-strand	160	1	8
β-strand	164-165	2	7
β-strand	173-181	9	6
β-strand	188-194	7	6
β-strand	202-208	7	9
β-strand	212-214	3	10
β-strand	221-229	9	9
α-helix	233	1
β-strand	234	1	9
α-helix	235	1
β-strand	237-247	11	10
β-strand	250-253	4	10
α-helix	255-257	3
β-strand	259-263	5	10
β-strand	264	1	9
β-strand	267-272	6	9
α-helix	274-280	7
α-helix	284-287	4
β-strand	291-300	10	10
β-strand	306-317	12	10
β-strand	322-324	3	11
β-strand	331-332	2	12
β-strand	338-345	8	11
β-strand	351	1	11
β-strand	356-359	4	12
α-helix	360-362	3
β-strand	364-367	4	12
β-strand	373-378	6	11
β-strand	386-393	8	12
α-helix	400-402	3
β-strand	405-412	8	12
α-helix	413-415	3
α-helix	416-418	3
β-strand	422-427	6	13
β-strand	437-445	9	13
α-helix	448-452	5
β-strand	456-463	8	14
β-strand	466-474	9	14
β-strand	481-487	7	13
α-helix	490-492	3
β-strand	495-504	10	14
β-strand	508-517	10	14
β-strand	526-529	4	15
β-strand	535	1	16
β-strand	540-547	8	15
β-strand	552-559	8	17
α-helix	560-565	6
α-helix	573-582	10
β-strand	590	1	14
α-helix	595-602	8
β-strand	604-608	5	1
α-helix	614-617	4

Chain B: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	718-719	2
α-helix	720-722	3
β-strand	726	1	18
β-strand	732-733	2	17
β-strand	737-739	3	17
α-helix	743-744	2
β-strand	750-757	8	15
β-strand	764-773	10	17
β-strand	777-780	4	17
α-helix	781-783	3
β-strand	784-787	4	17
β-strand	788	1	16
β-strand	792-796	5	19
β-strand	802-803	2	18
β-strand	808-816	9	19
β-strand	822-828	7	18
α-helix	829-830	2
β-strand	834-836	3	19
β-strand	844-850	7	18
β-strand	854-864	11	19
β-strand	868-878	11	18
β-strand	884-894	11	18
α-helix	895	1
β-strand	898-908	11	20
α-helix	910-913	4
β-strand	918-923	6	21
β-strand	931	1	20
α-helix	932	1
β-strand	937-945	9	20

Chain C: 14 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	1252-1258	7	21
β-strand	1266-1271	6	21
α-helix	1272-1274	3
β-strand	1277	1	6
β-strand	1279-1283	5	20
β-strand	1289-1295	7	21
β-strand	1299-1309	11	20
β-strand	1321-1329	9	22
β-strand	1341-1349	9	22
α-helix	1354	1
β-strand	1355-1363	9	23
α-helix	1364-1365	2
β-strand	1368-1370	3	22
β-strand	1371	1	24
α-helix	1372-1379	8
β-strand	1384-1386	3	23
β-strand	1391-1392	2	24
β-strand	1395-1396	2	24
β-strand	1400-1408	9	23
β-strand	1414-1422	9	22
α-helix	1429-1431	3
β-strand	1432-1438	7	23
β-strand	1441	1	23
β-strand	1447-1450	4	23
β-strand	1451	1	25
β-strand	1454	1	25
α-helix	1458-1460	3
β-strand	1461-1464	4	26
β-strand	1467-1470	4	26
α-helix	1475-1476	2
β-strand	1479	1	27
α-helix	1486-1493	8
β-strand	1500-1512	13	27
β-strand	1515-1527	13	27
α-helix	1534-1536	3
β-strand	1539-1544	6	27
α-helix	1545-1547	3
α-helix	1548-1551	4
β-strand	1558-1563	6	27
α-helix	1565-1567	3
β-strand	1568	1	27
β-strand	1575-1578	4	27
β-strand	1584-1588	5	27
α-helix	1592-1595	4
α-helix	1600-1616	17

Chain D: 30 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	28
β-strand	23-27	5	29
α-helix	28-30	3
β-strand	32-36	5	29
β-strand	41-44	4	28
β-strand	48-50	3	29
β-strand	51	1	30
β-strand	57	1	30
β-strand	60-61	2	31
β-strand	67-68	2	31
β-strand	72-75	4	28
β-strand	77-78	2	32
α-helix	79-81	3
β-strand	87-90	4	33
β-strand	96-97	2	32
β-strand	101-106	6	33
α-helix	107	1
β-strand	111-113	3	34
β-strand	117-119	3	33
β-strand	120	1	35
β-strand	126	1	35
β-strand	132-134	3	34
α-helix	141-142	2
β-strand	149-152	4	36
β-strand	161-166	6	36
α-helix	167	1
β-strand	168	1	37
β-strand	170	1	37
β-strand	171-173	3	38
β-strand	177-179	3	36
β-strand	180	1	39
β-strand	186	1	39
β-strand	192-194	3	38
β-strand	200	1	40
α-helix	202-213	12
β-strand	215	1	41
β-strand	235	1	41
β-strand	243-251	9	42
α-helix	258-277	20
α-helix	282	1
β-strand	283-289	7	42
β-strand	293-297	5	42
α-helix	302-305	4
α-helix	307-314	8
α-helix	319-322	4
α-helix	330-341	12
α-helix	348-349	2
α-helix	352-354	3
β-strand	355-363	9	42
α-helix	374-383	10
α-helix	395-397	3
β-strand	398-404	7	42
α-helix	411-417	7
β-strand	427-428	2	42
β-strand	430	1	40
α-helix	433-447	15
β-strand	471-476	6	43
β-strand	486-490	5	43
β-strand	495-498	4	43
α-helix	500-502	3
β-strand	512-516	5	43
β-strand	523-530	8	43
α-helix	540-542	3
β-strand	553-557	5	43
α-helix	569-570	2
β-strand	571	1	44
β-strand	575	1	45
α-helix	576-581	6
α-helix	590-597	8
β-strand	602-610	9	44
β-strand	615-623	9	44
α-helix	628-633	6
α-helix	634-637	4
α-helix	647-649	3
β-strand	655-659	5	44
α-helix	671-673	3
α-helix	676	1
β-strand	677-682	6	44
β-strand	685-695	11	44
β-strand	714-719	6	44
α-helix	720-722	3
α-helix	724-730	7
β-strand	738	1	45

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cobra venom factor	A	protein	627	Naja kaouthia	Q91132 (AlphaFold model)
Cobra venom factor	B	protein	252	Naja kaouthia	Q91132 (AlphaFold model)
Cobra venom factor	C	protein	379	Naja kaouthia	Q91132 (AlphaFold model)
Complement factor B	D	protein	741	Homo sapiens	P00751 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3HRZ_1 Cobra venom factor (chains A)
ALYTLITPAVLRTDTEEQILVEAHGDSTPKQLDIFVHDFPRKQKTLFQTRVDMNPAGGML
VTPTIEIPAKEVSTDSRQNQYVVVQVTGPQVRLEKVVLLSYQSSFLFIQTDKGIYTPGSP
VLYRVFSMDHNTSKMNKTVIVEFQTPEGILVSSNSVDLNFFWPYNLPDLVSLGTWRIVAK
YEHSPENYTAYFDVRKYVLPSFEVRLQPSEKFFYIDGNENFHVSITARYLYGEEVEGVAF
VLFGVKIDDAKKSIPDSLTRIPIIDGDGKATLKRDTFRSRFPNLNELVGHTLYASVTVMT
ESGSDMVVTEQSGIHIVASPYQIHFTKTPKYFKPGMPYELTVYVTNPDGSPAAHVPVVSE
AFHSMGTTLSDGTAKLILNIPLNAQSLPITVRTNHGDLPRERQATKSMTAIAYQTQGGSG
NYLHVAITSTEIKPGDNLPVNFNVKGNANSLKQIKYFTYLILNKGKIFKVGRQPRRDGQN
LVTMNLHITPDLIPSFRFVAYYQVGNNEIVADSVWVDVKDTCMGTLVVKGDNLIQMPGAA
MKIKLEGDPGARVGLVAVDKAVYVLNDKYKISQAKIWDTIEKSDFGCTAGSGQNNLGVFE
DAGLALTTSTNLNTKQRSAAKCPQPAN

Sequence of entity 2 (B), FASTA

>3HRZ_2 Cobra venom factor (chains B)
DDNEDGFIADSDIISRSDFPKSWLWLTKDLTEEPNSQGISSKTMSFYLRDSITTWVVLAV
SFTPTKGICVAEPYEIRVMKVFFIDLQMPYSVVKNEQVEIRAILHNYVNEDIYVRVELLY
NPAFCSASTKGQRYRQQFPIKALSSRAVPFVIVPLEQGLHDVEIKASVQEALWSDGVRKK
LKVVPEGVQKSIVTIVKLDPRAKGVGGTQLEVIKARKLDDRVPDTEIETKIIIQGDPVAQ
IIENSIDGSKLN

Sequence of entity 3 (C), FASTA

>3HRZ_3 Cobra venom factor (chains C)
EIQMPTHKDLNLDITIELPDREVPIRYRINYENALLARTVETKLNQDITVTASGDGKATM
TILTFYNAQLQEKANVCNKFHLNVSVENIHLNAMGAKGALMLKICTRYLGEVDSTMTIID
ISMLTGFLPDAEDLTRLSKGVDRYISRYEVDNNMAQKVAVIIYLNKVSHSEDECLHFKIL
KHFEVGFIQPGSVKVYSYYNLDEKCTKFYHPDKGTGLLNKICIGNVCRCAGETCSSLNHQ
ERIDVPLQIEKACETNVDYVYKTKLLRIEEQDGNDIYVMDVLEVIKQGTDENPRAKTHQY
ISQRKCQEALNLKVNDDYLIWGSRSDLLPTKDKISYIITKNTWIERWPHEDECQEEEFQK
LCDDFAQFSYTLTEFGCPT

Sequence of entity 4 (D), FASTA

>3HRZ_4 Complement factor B (chains D)
TPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYVCPSGFYPYPVQTRTCRSTGSWSTL
KTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVSDEISFHCYDGYTLRGSANRTC
QVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDSVTYHCSRGLTLRGSQRRTC
QEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAEDGHGPGEQQKRKIVLDP
SGSMNIYLVLDGSGSIGASDFTGAKKCLVNLIEKVASYGVKPRYGLVTYATYPKIWVKVS
EADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNRTRHVII
LMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALASK
KDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKISVIRPS
KGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKK
EAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPA
QDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGG
VSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINL
FQVLPWLKEKLQDEDLGFLAA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
PO4	Phosphate ion	O4 P	5

Water and common crystallization additives (P6G, K) are not listed.

Primary citation

Insights into complement convertase formation based on the structure of the factor B-cobra venom factor complex. Janssen, B.J., Gomes, L., Koning, R.I. et al. EMBO J (2009) 28:2469-2478. DOI 10.1038/emboj.2009.184 · PubMed

Other PDB entries of the same protein (UniProt Q91132 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FRP 2.61 Å, Crystal Structure of Cobra Venom Factor, a Co-factor for C3- and C5 convertase CVFBb
3HS0 3.0 Å, Cobra Venom Factor (CVF) in complex with human factor B
8AYH 3.35 Å, Structure of Complement C5 in Complex with small molecule inhibitor and CVF
3PRX 4.3 Å, Structure of Complement C5 in Complex with CVF and SSL7
9TDL 4.3 Å, Complex between complement C5 and cobra venom factor, re-refined

Browse structure collections

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