7P2D: AlphaMbeta2/Cd11bCD18 headpiece

Structure of alphaMbeta2/Cd11bCD18 headpiece in complex with a nanobody. Determined by X-ray diffraction at 3.2 Å resolution. Released 4 May 2022.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Lama glama
Chains: 3
Atoms: 10,419
Mol. weight: 152.83 kDa
Ligands: NAG, CA
Released: 4 May 2022

Explore 7P2D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P2D contains 51 α-helices and 101 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: 24 helices, 60 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-12	4	2
β-strand	22-24	3	3
β-strand	29-34	6	3
β-strand	46-51	6	3
β-strand	57-59	3	3
β-strand	69	1	4
β-strand	76-80	5	4
β-strand	85-97	13	4
β-strand	100-110	11	4
β-strand	119-121	3	4
α-helix	128-130	3
β-strand	133-140	8	5
α-helix	147-164	18
β-strand	169-176	8	5
β-strand	180-184	5	5
α-helix	186-191	6
α-helix	195-199	5
α-helix	211-217	7
α-helix	218-222	5
α-helix	225-227	3
α-helix	229-230	2
β-strand	234-241	8	5
α-helix	252-261	10
β-strand	265-271	7	5
α-helix	273-275	3
α-helix	278-287	10
α-helix	289	1
α-helix	292-295	4
β-strand	296-299	4	5
α-helix	302-304	3
α-helix	305-320	16
β-strand	337-343	7	6
β-strand	348-352	5	6
β-strand	360	1	7
β-strand	361-364	4	6
β-strand	374	1	6
β-strand	388	1	7
β-strand	392-397	6	8
β-strand	400-410	11	8
β-strand	413-422	10	8
β-strand	425-433	9	8
β-strand	444-448	5	9
β-strand	458-463	6	9
β-strand	468	1	10
β-strand	471	1	10
β-strand	473	1	11
β-strand	474-479	6	9
α-helix	480-481	2
α-helix	486-488	3
β-strand	492-494	3	9
β-strand	505	1	11
β-strand	508-513	6	12
β-strand	522-527	6	12
α-helix	530-533	4
β-strand	536-540	5	12
β-strand	542-543	2	13
β-strand	547-548	2	13
β-strand	554-557	4	12
α-helix	558-561	4
β-strand	571-574	4	2
β-strand	586-589	4	2
β-strand	593-597	5	2
α-helix	598	1
β-strand	599	1	1
α-helix	600-601	2
β-strand	602-610	9	14
β-strand	630-631	2	15
β-strand	635	1	16
β-strand	637-644	8	14
β-strand	657-665	9	17
β-strand	675-676	2	18
β-strand	684-690	7	17
β-strand	695-697	3	14
β-strand	700	1	16
β-strand	701-702	2	18
β-strand	703-704	2	15
α-helix	713	1
β-strand	714-719	6	17
β-strand	722-724	3	17
α-helix	725-727	3
α-helix	733-735	3
β-strand	736-737	2	14
β-strand	744-749	6	17

Chain B: 24 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	11-16	6
β-strand	22-24	3	19
α-helix	36-39	4
β-strand	40-41	2	19
α-helix	43-48	6
β-strand	56-57	2	19
β-strand	62-65	4	20
α-helix	67-69	3
β-strand	76-77	2	21
β-strand	80-85	6	20
α-helix	86	1
β-strand	90-98	9	21
β-strand	99	1	22
β-strand	106-112	7	23
α-helix	115-117	3
α-helix	118-127	10
α-helix	129-138	10
β-strand	143-149	7	23
α-helix	162-166	5
β-strand	176	1	24
α-helix	177-179	3
β-strand	182-189	8	23
α-helix	192-200	9
α-helix	202-203	2
β-strand	204	1	24
β-strand	212	1	25
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-241	7	23
β-strand	245	1	25
α-helix	250-254	5
α-helix	259-260	2
β-strand	267	1	23
β-strand	270	1	23
α-helix	278-281	4
α-helix	282-291	10
β-strand	294-301	8	23
α-helix	302-304	3
α-helix	305-309	5
α-helix	310-312	3
β-strand	319-323	5	23
α-helix	331-343	13
β-strand	345-349	5	20
β-strand	356-363	8	21
β-strand	369-373	5	21
β-strand	376-378	3	20
β-strand	383	1	22
β-strand	386-395	10	21
α-helix	399-401	3
β-strand	402-409	8	20
β-strand	414-421	8	20
α-helix	427-429	3
β-strand	437	1	26
β-strand	440	1	26

Chain C: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	27
β-strand	11-14	4	28
β-strand	19-26	8	27
α-helix	29-31	3
β-strand	35-40	6	28
β-strand	47-52	6	28
β-strand	58-60	3	28
α-helix	62-64	3
β-strand	68-73	6	27
β-strand	78-83	6	27
α-helix	88-90	3
β-strand	92-98	7	28
β-strand	110-111	2	28
β-strand	115-120	6	28

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	B	protein	473	Homo sapiens	P05107 (AlphaFold model)
hCD11bNb1 nanobody	C	protein	129	Lama glama

Sequence of entity 1 (A), FASTA

>7P2D_1 Isoform 2 of Integrin alpha-M (chains A)
FNLDTENAMTFQENARGFGQSVVQLQGSRVVVGAPQEIVAANQRGSLYQCDYSTGSCEPI
RLQVPVEAVNMSLGLSLAATTSPPQLLACGPTVHQTCSENTYVKGLCFLFGSNLRQQPQK
FPEALRGCPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEF
RIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFRITNGARKNAFKILVVI
TDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVN
NFEALKTIQNQLREKIFAIEGTQTGSSSSFEHEMSQEGFSAAITSNGPLLSTVGSYDWAG
GVFLYTSKEKSTFINMTRVDSDMNDAYLGYAAAIILRNRVQSLVLGAPRYQHIGLVAMFR
QNTGMWESNANVKGTQIGAYFGASLCSVDVDSNGSTDLVLIGAPHYYEQTRGGQVSVCPL
PRGQRARWQCDAVLYGEQGQPWGRFGAALTVLGDVNGDKLTDVAIGAPGEEDNRGAVYLF
HGTSGSGISPSHSQRIAGSKLSPRLQYFGQSLSGGQDLTMDGLVDLTVGAQGHVLLLRSQ
PVLRVKAIMEFNPREVARNVFECNDQVVKGKEAGEVRVCLHVQKSTRDRLREGQIQSVVT
YDLALDSGRPHSRAVFNETKRSTRRQTQVLGLTQTCETLKLQLPNCIEDPVSPIVLRLNF
SLVGTPLSAFGNLRPVLAEDAQRLFTALFPFEKNTGGLEVLFQ

Sequence of entity 2 (B), FASTA

>7P2D_2 Integrin beta (chains B)
QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPT
SLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDD
LRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPF
AFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRNVTRLLVFA
TDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAV
TSRMVKTYEKLTEIIPKSAVGELSEDSSNVVHLIKNAYNKLSSRVFLDHNALPDTLKVTY
DSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVL
PQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCEKNCEPAALQTLFQ

Sequence of entity 3 (C), FASTA

>7P2D_3 hCD11bNb1 nanobody (chains C)
MQVQLVETGGGLVQAGGSLRLSCAASGNINSFNAMGWFRQAPGKQRELVAAITFGGRTNY
ADSVKGRFTISRDNTKGSVYLQMNSLKPEDTAVYYCAASENNLLTGVWHYWGRGTQVTVS
SLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
CA	Calcium ion	Ca	2

Primary citation

Structural insights into the function-modulating effects of nanobody binding to the integrin receptor alpha M beta 2. Jensen, R.K., Pedersen, H., Lorentzen, J. et al. J Biol Chem (2022) 298:102168-102168. DOI 10.1016/j.jbc.2022.102168 · 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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