9Y7C: HB3VAR03 CIDRa1.4

HB3VAR03 CIDRa1.4 in complex with B57 and C50 fabs. Determined by electron microscopy at 3.4 Å resolution. Released 23 Sept 2026.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, Plasmodium falciparum HB3
Chains: 5
Atoms: 5,017
Mol. weight: 194 kDa
Released: 23 Sept 2026

Explore 9Y7C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y7C contains 16 α-helices and 53 β-strands across 5 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	504-505	2	14
β-strand	508	1	15
α-helix	518-521	4
α-helix	523-527	5
β-strand	538	1	15
β-strand	541-542	2	14
β-strand	552-554	3	14
β-strand	568-570	3	14
α-helix	571-595	25
α-helix	608-630	23
α-helix	641-643	3
α-helix	647-653	7
α-helix	655-661	7
α-helix	665-683	19
α-helix	695-712	18

Chain B: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	11-12	2	8
β-strand	19-24	6	7
β-strand	33	1	9
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	57-59	3	10
β-strand	68-72	5	7
β-strand	77-81	5	7
α-helix	84-86	3
β-strand	88-92	5	10
β-strand	95	1	9
α-helix	99-100A	3
β-strand	100D	1	9
β-strand	102	1	11
β-strand	107-109	3	10
β-strand	110-111	2	8

Chain C: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	12
β-strand	18-22	5	13
α-helix	23-24	2
β-strand	34-38	5	11
β-strand	45-48	4	11
β-strand	62-65	4	13
β-strand	72-76	5	13
α-helix	80-82	3
β-strand	84-92	9	11
β-strand	95B-98	4	11
α-helix	99-101	3
β-strand	102-104	3	11
β-strand	105-106	2	12

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	22-25	4	1
β-strand	34-39	6	3
β-strand	45-51	7	3
α-helix	61-63	3
β-strand	71-72	2	1
β-strand	77-78	2	1
β-strand	89-92	4	3
β-strand	94-95	2	4
β-strand	100E-102	3	4
β-strand	104	1	1
β-strand	109-111	3	2

Chain L: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	5
β-strand	9-13	4	6
β-strand	18-24	7	5
β-strand	33-38	6	6
β-strand	45-48	4	6
β-strand	62-67	6	5
β-strand	70-76	7	5
α-helix	80-82	3
β-strand	85-92	8	6
β-strand	95A-97	3	6
β-strand	103-106	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B57 heavy chain	H	protein	122	Homo sapiens
B57 light chain	L	protein	110	Homo sapiens
C50 heavy chain	B	protein	121	Homo sapiens
C50 light chain	C	protein	101	Homo sapiens
PfEMP1	A	protein	1260	Plasmodium falciparum HB3	A0A0L7KL67

Sequence of entity 1 (H), FASTA

>9Y7C_1 B57 heavy chain (chains H)
QVQLVQSGAEVRKPGSSVKVSCKVSGGTFSIFGINWIRKAPGQGFEWMGGIVPQLGGPNY
VKKFQGRVSFTADELTTTAYMELRSLTPEDSALYFCAKGAQTYALLYYFDSWGQGTLVTV
SS

Sequence of entity 2 (L), FASTA

>9Y7C_2 B57 light chain (chains L)
QSALTQPPSASGSPGQSVTISCTGTSSDIGGYNYVSWYQQHPGKAPKVVIYDVTKRPSGV
PDRFSGSKSGNTASLTVSGLQADDEAIYYCSSYAYNNNLVFGGGTSLAVL

Sequence of entity 3 (B), FASTA

>9Y7C_3 C50 heavy chain (chains B)
QVQLVESGGGVVQPGRSLRLSCAASGFTFETYVMHWVRQTPGKGLEWVALTSYDGKRKYY
ADSVKGRFSASRDNSENTVSLQMSSLSTEDTAVYYCVRSRHGYSFTNMDVWGRGTTVIVS
S

Sequence of entity 4 (C), FASTA

>9Y7C_4 C50 light chain (chains C)
VSAAPGQTVTISCSEYISNIGDNYVSWYQHVPGTAPRVVMSHYNERPSGIPDRFSGSKSG
ASATLGITGLQTGDEADYYCGAWDDRLKIFVFGTATKVTVL

Sequence of entity 5 (A), FASTA

>9Y7C_5 PfEMP1 (chains A)
MGSSASKFSKIVVGNETHKSARNVLEGFAKDIKGKASIDAEKHAYSLKGNLKDAKFNHDF
FKIKSDMPGNPCYLDFAFHSNTPGNQREYRHPCARSMNKNLFNLEGAVCTNSKIKGNEEK
INGAGACAPYRRRHICDLNLEHIDVHNVQNIHDLLGNVLVTAKYEGESIVEKHPNRGSSE
VCTALARSFADIGDIIRGKDLYLGHEQGNNKLEARLKTIFQNIKNKNKSPLDKLSLEQVR
EYWWALNREDVWKALTCFADGSEEYFIQSSDKEHSFSSEYCGHEQGNVPTNLDYVPQFLR
WFDEWADDFCRIKKIKLENVKNACRDEKKRKYCSLNGFDCTQTIWKKGVLHRSNECTGCL
VKCNPYEIWLGNQREAFRKQKEKYENEIKTYVHDTGISNSNINNEYYKEFYKILKNNNYE
TANEFIKLLNEGRYCNKKEKIEEEEDIDFTNTNEKGTFYRSDYCQVCPDCGVECKNETCT
PKTVIYPDCGKNEKYEPPGDAKNTEINVINSGDKEGYIFEKLSEFCTNENNENGKNYEQW
KCYYDNKKNNNKCKMEINIANSKLKNKVTSFDEFFDFWVRKLLIDTIKWETELTYCINNT
DVTDCNKCNKNCVCFDKWVKQKEDEWTNIMKLFTNKHDIPKKYYLNINDLFDSFFFQVIY
KFNEGEAKWNELKENLKKQIASSKANNGTKDSEAAIKVLFNHIKEIATICKDNNTNEGCD
PSVDSKTNSCGKNTKAGSDKVISVKQIAQYYKRIAHKQLNERGSRSALKGDASKGTYKKN
GTPSNLKEICEITAKHSNDSRRDGEPCTGKDGGQVRVRTKIGTPWTKIVEINKTSYKEVF
LPPRRQHMCTSNLEHLNTGNKGLKDGKLAIHSLLGDVLLAAKEQANFIKNKYKRQKASNG
FKDKGTICRAIRYSYADLGDIIKGTDLWEANPGEKNTQRRLKTVFGIIKKNMPGIKDNQK
YKDDEKNNPPYKLLREDWWEANRDQVWQAMKCAMKNGITCGSSDHTPLDDYIPQKLRWLT
EWAEWYCKAQSKEYEKLKEKCKECKGNDQCTQDTPDCEKCKAACKKYGKNIKTWEDQWKV
ISSKYKELYKQAEIYAGNGGPGYYNTKVQEEDKPVVDFLYNLYLQNGGKKGPPPDTHPSK
SVTAPLKQVATVDTPSTVYSTPEGYIHQEAAMDCKQQHVFCDDNSGGKDDNKQYAFRHQP
HDYDEALRCDQRDKPPPESKKVEKAKKEKDENDDGGSHHHHHHGGGSAHIVMVDAYKPTK

Primary citation

Structure of variant specific human monoclonal antibody B57 in complex with HB3VAR03 CIDRa1.4 PfEMP1 protein. Raghavan, S.S.R., Ward, A.B. To be published.

Other PDB entries of the same protein (UniProt A0A0L7KL67), best resolution first:

8C44 3.2 Å, HB3VAR03 apo headstructure (PfEMP1 A) complexed with EPCR
8C3Y 3.8 Å, HB3VAR03 apo headstructure (PfEMP1 A)

Browse structure collections

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