9T5Z: AlphaM/beta2:MEM148-Fab headpiece complex

Cryo-EM structure of alphaM/beta2:MEM148-Fab headpiece complex (without alphaM I-domain). Determined by electron microscopy at 3.1 Å resolution. Released 25 Mar 2026.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 10,752
Mol. weight: 187.46 kDa
Ligands: MN, CA, NAG
Released: 25 Mar 2026

Explore 9T5Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9T5Z contains 31 α-helices and 127 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: 8 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-11	3	2
β-strand	21-24	4	3
β-strand	29-33	5	3
β-strand	38-40	3	4
β-strand	43-44	2	4
β-strand	45	1	5
β-strand	47-51	5	3
β-strand	57-59	3	3
α-helix	60-61	2
β-strand	73	1	5
β-strand	76-80	5	6
β-strand	85-96	12	6
β-strand	101-110	10	6
α-helix	117-118	2
β-strand	119-120	2	6
β-strand	338	1	7
β-strand	342-343	2	7
β-strand	348-351	4	7
α-helix	355-358	4
β-strand	362-365	4	7
β-strand	371-374	4	7
β-strand	391-396	6	8
β-strand	401-407	7	8
α-helix	410-412	3
β-strand	414	1	9
β-strand	415-422	8	8
β-strand	425-433	9	8
β-strand	441	1	9
β-strand	444-448	5	10
β-strand	458-467	10	10
β-strand	472	1	10
β-strand	473	1	11
β-strand	474-479	6	10
α-helix	486-487	2
β-strand	491-493	3	10
β-strand	504	1	11
β-strand	508-512	5	12
β-strand	521-525	5	12
α-helix	529-532	4
β-strand	534	1	13
β-strand	535-539	5	12
β-strand	541-542	2	14
β-strand	546-547	2	14
β-strand	553-556	4	12
β-strand	567	1	13
β-strand	571-573	3	2
β-strand	584-589	6	2
β-strand	592-597	6	2
β-strand	598	1	1
β-strand	601-609	9	15
β-strand	629-630	2	16
β-strand	635-643	9	15
β-strand	656-664	9	17
β-strand	674-675	2	18
β-strand	683-689	7	17
β-strand	694-698	5	15
β-strand	700-701	2	18
β-strand	702-703	2	16
α-helix	712	1
β-strand	713-723	11	17
α-helix	724-726	3
β-strand	735-736	2	15
β-strand	744-748	5	17

Chain B: 13 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	62-66	5	19
β-strand	76-77	2	20
β-strand	80-84	5	19
β-strand	90-97	8	20
β-strand	99	1	21
α-helix	102-104	3
β-strand	105-112	8	22
α-helix	115-118	4
α-helix	121-138	18
β-strand	142-149	8	22
β-strand	183-189	7	22
α-helix	192-201	10
β-strand	212	1	23
α-helix	214-222	9
α-helix	225-228	4
β-strand	234-241	8	22
β-strand	245	1	23
α-helix	250-254	5
β-strand	266	1	24
β-strand	270	1	22
β-strand	271	1	24
α-helix	272-276	5
α-helix	278-281	4
α-helix	282-292	11
β-strand	294-300	7	22
α-helix	302-304	3
α-helix	305-312	8
β-strand	320-322	3	22
α-helix	328-338	11
β-strand	344-349	6	19
β-strand	350	1	25
β-strand	356-363	8	20
β-strand	369-373	5	20
β-strand	376-379	4	19
β-strand	383	1	21
β-strand	387-395	9	20
β-strand	402-408	7	19
β-strand	414-420	7	19

Chain H: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	11-12	2	27
β-strand	18-25	8	26
β-strand	33-40	8	28
β-strand	44-51	8	28
β-strand	55	1	25
β-strand	57-59	3	28
β-strand	67-72	6	26
β-strand	77-82	6	26
α-helix	87-89	3
β-strand	91-98	8	28
β-strand	105	1	28
β-strand	110-112	3	28
β-strand	113-114	2	27
β-strand	120	1	29
β-strand	123-127	5	30
β-strand	138-148	11	30
β-strand	149	1	29
β-strand	154-157	4	31
β-strand	166-168	3	30
α-helix	169-171	3
β-strand	172-174	3	30
β-strand	177-187	11	30
β-strand	197-202	6	31
α-helix	203-205	3
β-strand	207-212	6	31
α-helix	214-216	3

Chain L: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	32
β-strand	11-12	2	33
β-strand	19-25	7	32
β-strand	33-38	6	34
β-strand	45-49	5	34
β-strand	53	1	34
β-strand	62-67	6	32
β-strand	70-75	6	32
β-strand	85-90	6	34
α-helix	96	1
β-strand	97	1	28
β-strand	98	1	34
β-strand	102-103	2	34
β-strand	104-105	2	33
β-strand	111	1	35
β-strand	114-118	5	36
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	36
β-strand	140	1	35
β-strand	145-150	6	37
β-strand	153-155	3	37
β-strand	159-163	5	36
α-helix	164-167	4
β-strand	173-182	10	36
α-helix	183-188	6
β-strand	191-198	8	37
β-strand	201-210	10	37
α-helix	211-213	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-M	A	protein	762	Homo sapiens	P11215 (AlphaFold model)
Integrin beta-2	B	protein	469	Homo sapiens	P05107 (AlphaFold model)
Murine IgG1 MEM148 heavy chain	H	protein	218	Mus musculus
Anti-colorectal carcinoma light chain	L	protein	214	Mus musculus

Sequence of entity 1 (A), FASTA

>9T5Z_1 Integrin alpha-M (chains A)
FNLDTENAMTFQENARGFGQSVVQLQGSRVVVGAPQEIVAANQRGSLYQCDYSTGSCEPI
RLQVPVEAVNMSLGLSLAATTSPPQLLACGPTVHQTCSENTYVKGLCFLFGSNLRQQPQK
FPEALRGCPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEF
RIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFRITNGARKNAFKILVVI
TDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVN
NFEALKTIQNQLREKIFAIEGTQTGSSSSFEHEMSQEGFSAAITSNGPLLSTVGSYDWAG
GVFLYTSKEKSTFINMTRVDSDMNDAYLGYAAAIILRNRVQSLVLGAPRYQHIGLVAMFR
QNTGMWESNANVKGTQIGAYFGASLCSVDVDSNGSTDLVLIGAPHYYEQTRGGQVSVCPL
PRGRTRWQCDAVLYGEQGQPWGRFGAALTVLGDVNGDKLTDVAIGAPGEEDNRGAVYLFH
GTSGSGISPSHSQRIAGSKLSPRLQYFGQSLSGGQDLTMDGLVDLTVGAQGHVLLLRSQP
VLRVKAIMEFNPREVARNVFECNDQVVKGKEAGEVRVCLHVQKSTRDRLREGQIQSVVTY
DLALDSGRPHSRAVFNETKRSTRRQTQVLGLTQTCETLKLQLPNCIEDPVSPIVLRLNFS
LVGTPLSAFGNLRPVLAEDAQRLFTALFPFEKNTGGLEVLFQ

Sequence of entity 2 (B), FASTA

>9T5Z_2 Integrin beta-2 (chains B)
QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPT
SLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDD
LRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPF
AFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRNVTRLLVFA
TDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAV
TSRMVKTYEKLTEIIPKSAVGELSEDSSNVVHLIKNAYNKLSSRVFLDHNALPDTLKVTY
DSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVL
PQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCEPAALQTLFQ

Sequence of entity 3 (H), FASTA

>9T5Z_3 Murine IgG1 MEM148 heavy chain (chains H)
EVQLQESGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPYNKLEYMGYISYSGSTYYN
PSLESRVSITRDTSKNQYYLQLHSVTTEDTATYHCARERDYAFDFWGQGTTLTVSSAKTT
PPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 4 (L), FASTA

>9T5Z_4 Anti-colorectal carcinoma light chain (chains L)
DIKMTQSPSPMYASLGERVTVTCKASQDINNYLSWFQQKPGKSPKTLIYRAKRLVDGVPS
RFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPLTFGAGTKLELKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	1
CA	Calcium ion	Ca	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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

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