9T5V: AlphaM/beta2:C3d-anti-CR3-Nb headpiece complex

Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO1 3D class reconstruction). Determined by electron microscopy at 3.06 Å resolution. Released 25 Mar 2026.

Method: Electron microscopy
Resolution: 3.06 Å
Organisms: Homo sapiens, Lama glama
Chains: 3
Atoms: 12,937
Mol. weight: 189.67 kDa
Ligands: NAG, MN, CA
Released: 25 Mar 2026

Explore 9T5V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9T5V contains 60 α-helices and 112 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: 22 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-11	3	2
β-strand	22-24	3	3
α-helix	25	1
β-strand	29-40	12	3
β-strand	43-44	2	3
β-strand	45	1	4
β-strand	46-51	6	3
β-strand	57-59	3	3
α-helix	60-61	2
β-strand	73	1	4
β-strand	76-80	5	5
β-strand	85-96	12	5
β-strand	101-110	10	5
β-strand	119-120	2	5
β-strand	130	1	6
β-strand	133-140	8	7
α-helix	147-164	18
β-strand	169-176	8	7
β-strand	180-184	5	7
α-helix	186-191	6
α-helix	196-199	4
β-strand	209	1	8
α-helix	211-221	11
α-helix	225-227	3
β-strand	234-241	8	7
β-strand	246	1	8
α-helix	256-261	6
β-strand	265-270	6	7
α-helix	278-287	10
α-helix	289	1
β-strand	296-298	3	7
α-helix	304-310	7
α-helix	312-313	2
β-strand	314	1	6
α-helix	315	1
β-strand	317	1	9
β-strand	328	1	9
β-strand	338	1	10
β-strand	342-343	2	10
β-strand	348-352	5	10
α-helix	355-358	4
β-strand	360	1	11
β-strand	361-365	5	10
β-strand	371-374	4	10
α-helix	376-378	3
β-strand	388	1	11
β-strand	391-397	7	12
β-strand	400-407	8	12
α-helix	410-412	3
β-strand	414	1	13
β-strand	415-422	8	12
β-strand	425-433	9	12
β-strand	441	1	13
β-strand	444-448	5	14
β-strand	458-467	10	14
β-strand	472	1	14
β-strand	473	1	15
β-strand	474-479	6	14
β-strand	492-494	3	14
β-strand	505	1	15
β-strand	508-513	6	16
β-strand	522-527	6	16
α-helix	530-533	4
β-strand	536-540	5	16
α-helix	541	1
β-strand	542-543	2	17
β-strand	547-548	2	17
β-strand	554-557	4	16
α-helix	558-561	4
β-strand	572-576	5	2
β-strand	585-590	6	2
β-strand	593-598	6	2
β-strand	599	1	1
α-helix	600-601	2
β-strand	602-610	9	18
β-strand	630-631	2	19
β-strand	635-644	10	18
β-strand	657-665	9	20
β-strand	675-676	2	21
β-strand	683-690	8	20
α-helix	694	1
β-strand	695-700	6	18
β-strand	701-702	2	21
β-strand	703-704	2	19
β-strand	714-724	11	20
α-helix	725-727	3
β-strand	736-737	2	18
β-strand	745-749	5	20

Chain B: 20 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	11-17	7
β-strand	21-22	2	22
β-strand	24	1	23
α-helix	37-39	3
β-strand	41-42	2	22
α-helix	43-46	4
β-strand	56	1	23
β-strand	62-66	5	24
β-strand	76-77	2	25
β-strand	80-85	6	24
β-strand	87	1	25
β-strand	90-97	8	25
β-strand	99	1	26
α-helix	102-104	3
β-strand	105-112	8	27
α-helix	115-118	4
α-helix	121-138	18
β-strand	142-149	8	27
α-helix	177-179	3
β-strand	183-189	7	27
α-helix	192-200	9
β-strand	212	1	28
α-helix	214-223	10
α-helix	225-228	4
β-strand	234-241	8	27
β-strand	245	1	28
α-helix	251-254	4
α-helix	259-260	2
β-strand	266	1	29
β-strand	270	1	27
β-strand	271	1	29
α-helix	272-276	5
α-helix	278-281	4
α-helix	282-291	10
β-strand	294-300	7	27
α-helix	302-304	3
α-helix	305-312	8
β-strand	320-322	3	27
α-helix	328-339	12
β-strand	344-349	6	24
β-strand	356-363	8	25
β-strand	369-373	5	25
β-strand	376-379	4	24
β-strand	383	1	26
β-strand	387-395	9	25
α-helix	399-400	2
β-strand	402-408	7	24
β-strand	414-421	8	24
β-strand	437	1	30
β-strand	440	1	30
α-helix	444-446	3

Chain C: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	31
β-strand	11-13	3	32
β-strand	18-26	9	31
β-strand	33-40	8	32
β-strand	47-53	7	32
β-strand	57-60	4	32
α-helix	81-86	6
α-helix	94-114	21
α-helix	117-120	4
α-helix	122-141	20
β-strand	143-144	2	33
β-strand	148-149	2	33
α-helix	156-157	2
α-helix	159-171	13
α-helix	180-192	13
α-helix	214-216	3
α-helix	223-236	14
α-helix	248-262	15
α-helix	263-265	3
α-helix	269-280	12
α-helix	288-296	9
β-strand	298	1	34
β-strand	302	1	34
α-helix	309-325	17
α-helix	332-342	11
α-helix	352-367	16
β-strand	382-386	5	31
β-strand	391-397	7	31
α-helix	401-403	3
β-strand	405-413	9	32
α-helix	414-416	3
β-strand	430-434	5	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Integrin alpha-M	A	protein	763	Homo sapiens	P11215 (AlphaFold model)
Integrin beta-2	B	protein	469	Homo sapiens	P05107 (AlphaFold model)
C3d-anti-CR3-Nb fusion ligand	C	protein	448	Lama glama

Sequence of entity 1 (A), FASTA

>9T5V_1 Isoform 2 of Integrin alpha-M (chains A)
FNLDTENAMTFQENARGFGQSVVQLQGSRVVVGAPQEIVAANQRGSLYQCDYSTGSCEPI
RLQVPVEAVNMSLGLSLAATTSPPQLLACGPTVHQTCSENTYVKGLCFLFGSNLRQQPQK
FPEALRGCPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEF
RIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVI
TDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVN
NFEALKTIQNQLREKIFAIEGTQTGSSSSFEHEMSQEGFSAAITSNGPLLSTVGSYDWAG
GVFLYTSKEKSTFINMTRVDSDMNDAYLGYAAAIILRNRVQSLVLGAPRYQHIGLVAMFR
QNTGMWESNANVKGTQIGAYFGASLCSVDVDSNGSTDLVLIGAPHYYEQTRGGQVSVCPL
PRGQRARWQCDAVLYGEQGQPWGRFGAALTVLGDVNGDKLTDVAIGAPGEEDNRGAVYLF
HGTSGSGISPSHSQRIAGSKLSPRLQYFGQSLSGGQDLTMDGLVDLTVGAQGHVLLLRSQ
PVLRVKAIMEFNPREVARNVFECNDQVVKGKEAGEVRVCLHVQKSTRDRLREGQIQSVVT
YDLALDSGRPHSRAVFNETKNSTRRQTQVLGLTQTCETLKLQLPNCIEDPVSPIVLRLNF
SLVGTPLSAFGNLRPVLAEDAQRLFTALFPFEKNTGGENLYFQ

Sequence of entity 2 (B), FASTA

>9T5V_2 Integrin beta-2 (chains B)
QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPT
SLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDD
LRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPF
AFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRNVTRLLVFA
TDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAV
TSRMVKTYEKLTEIIPKSAVGELSEDSSNVVHLIKNAYNKLSSRVFLDHNALPDTLKVTY
DSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVL
PQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCEPAAENLYFQ

Sequence of entity 3 (C), FASTA

>9T5V_3 C3d-anti-CR3-Nb fusion ligand (chains C)
QVQLVESGGGLVQAGGSLRLSCTTSGFTFDDYAIGWFRQAPGKEREGVSCISSSEGKYYS
DGGGGSGGGGSGGGGSVDAERLKHLIVTPSGSGEQNMIGMTPTVIAVHYLDETEQWEKFG
LEKRQGALELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQ
VLCGAVKWLILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDIC
EEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKN
RWEDPGKQLYNVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQA
LAQYQKDAPDHKGGGGSGRFTISSDNAKNTVYLQMNNLKPEDTAVYYCAAEWNNFGRLCM
YPDYWGQGTQVTVSSENLYFQGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
MN	Manganese (II) ion	Mn	2
CA	Calcium ion	Ca	5

Primary citation

Three cryo-EM structures of complement C3d-bound alpha M beta 2 reveal an unexpected layer of dynamics for alpha I-containing integrin receptors. Lorentzen, J., Fruergaard, M.U., Lukacsi, S. et al. Sci Adv (2026) 12:eaea7241-eaea7241. DOI 10.1126/sciadv.aea7241 · PubMed

Other PDB entries of the same protein (UniProt P11215 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MF7 1.25 Å, Integrin alpha M I domain
1NA5 1.5 Å, Integrin alpha M I domain
8CE6 1.58 Å, Crystal structure of human Cd11b I domain in P212121 space group
1IDO 1.7 Å, I-domain from integrin CR3, MG2+ bound
1JLM 2.0 Å, I-domain from integrin CR3, MN2+ bound
4XW2 2.0 Å, Structural basis for simvastatin competitive antagonism of complement receptor 3
8CE9 2.11 Å, Crystal structure of human Cd11b I domain in C121 space group
1M1U 2.3 Å, An isoleucine-based allosteric switch controls affinity and shape shifting in integrin…
1N9Z 2.5 Å, Integrin alpha M I domain mutant
9RM9 2.6 Å, Cryo-EM structure of alphaM/beta2 headpiece complex without alphaM I-domain - the…
1BHO 2.7 Å, Mac-1 I domain magnesium complex
1BHQ 2.7 Å, Mac-1 I domain cadmium complex

Browse structure collections

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