4NEN: Integrin alpha-X

An internal ligand-bound, metastable state of a leukocyte integrin, aXb2. Determined by X-ray diffraction at 2.9 Å resolution. Released 15 Jan 2014.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 13,731
Mol. weight: 199.68 kDa
Ligands: CA, MG
Released: 15 Jan 2014

Explore 4NEN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NEN contains 59 α-helices and 137 β-strands across 2 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: 29 helices, 92 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-12	4	2
β-strand	21-25	5	3
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
β-strand	69	1	5
β-strand	73	1	4
β-strand	76-80	5	5
β-strand	85-97	13	5
β-strand	100-110	11	5
β-strand	117-119	3	5
α-helix	126-127	2
β-strand	128	1	6
α-helix	129-130	2
β-strand	131-138	8	7
α-helix	146-159	14
β-strand	167-174	8	7
β-strand	178-182	5	7
α-helix	184-189	6
α-helix	193-199	7
β-strand	207	1	8
α-helix	209-215	7
α-helix	216-220	5
α-helix	223-225	3
β-strand	232-239	8	7
β-strand	244	1	8
α-helix	250-259	10
β-strand	263-268	6	7
α-helix	270-272	3
α-helix	276-285	10
α-helix	287	1
α-helix	290-292	3
β-strand	294-296	3	7
α-helix	301-306	6
β-strand	310	1	6
β-strand	315	1	9
α-helix	317-319	3
β-strand	326	1	9
β-strand	335-342	8	10
β-strand	345-350	6	10
α-helix	353-356	4
β-strand	360-362	3	10
α-helix	368-369	2
β-strand	370-372	3	10
α-helix	379-381	3
β-strand	390-395	6	11
β-strand	398-405	8	11
α-helix	408-410	3
β-strand	413-419	7	11
β-strand	424-431	8	11
β-strand	443-446	4	12
β-strand	456-460	5	12
β-strand	465	1	13
β-strand	469-471	3	14
β-strand	473-477	5	12
α-helix	483-485	3
β-strand	489-491	3	12
β-strand	497-502	6	14
β-strand	505-508	4	15
β-strand	520-523	4	15
α-helix	527-530	4
β-strand	532	1	16
β-strand	533-537	5	15
β-strand	539-540	2	17
β-strand	544-545	2	17
β-strand	551-554	4	15
α-helix	555-558	4
β-strand	565	1	16
β-strand	569-573	5	2
β-strand	582-587	6	2
β-strand	590-595	6	2
β-strand	596	1	1
α-helix	597-598	2
β-strand	599-609	11	18
β-strand	613	1	19
β-strand	629-641	13	18
β-strand	654-662	9	18
β-strand	672-673	2	18
β-strand	680-687	8	18
β-strand	690-700	11	18
α-helix	710	1
β-strand	711-721	11	18
α-helix	722-723	2
β-strand	733-734	2	18
β-strand	742-746	5	18
β-strand	748	1	19
β-strand	762-767	6	20
β-strand	774-776	3	21
β-strand	779	1	21
β-strand	781-790	10	20
β-strand	795	1	22
β-strand	798-805	8	23
β-strand	808-811	4	20
β-strand	828-833	6	23
β-strand	839-846	8	23
β-strand	851	1	22
β-strand	856-865	10	20
β-strand	874-879	6	23
β-strand	882	1	23
β-strand	895-900	6	23
β-strand	901-905	5	21
β-strand	907-911	5	24
β-strand	918-921	4	25
β-strand	929-940	12	24
β-strand	946-958	13	25
β-strand	961-962	2	25
β-strand	964-970	7	24
β-strand	979-984	6	25
α-helix	991-997	7
β-strand	1000-1001	2	25
β-strand	1007-1018	12	25
β-strand	1023-1033	11	24
α-helix	1035-1039	5
β-strand	1044-1055	12	25
β-strand	1060-1062	3	21
α-helix	1063	1
α-helix	1067-1070	4
β-strand	1071-1080	10	25

Chain B: 30 helices, 45 β-strands

Element	Residues	Length	Sheet
α-helix	11-17	7
β-strand	22-24	3	26
α-helix	36-38	3
β-strand	40-41	2	26
α-helix	43-47	5
β-strand	56-57	2	26
β-strand	62-65	4	27
β-strand	76-77	2	28
β-strand	80-85	6	27
β-strand	87	1	28
α-helix	89-90	2
β-strand	91-97	7	28
β-strand	105-112	8	29
α-helix	115-117	3
α-helix	118-138	21
β-strand	143-149	7	29
α-helix	162-166	5
β-strand	176	1	30
β-strand	182-189	8	29
α-helix	192-200	9
β-strand	204	1	30
β-strand	212	1	31
α-helix	214-223	10
α-helix	225-228	4
β-strand	234-241	8	29
β-strand	245	1	31
α-helix	250-254	5
α-helix	258-260	3
β-strand	270	1	29
α-helix	272-275	4
α-helix	278-281	4
α-helix	282-291	10
β-strand	294-300	7	29
α-helix	302-304	3
α-helix	305-309	5
α-helix	311-314	4
β-strand	319-322	4	29
α-helix	323-324	2
α-helix	330-343	14
β-strand	345-349	5	27
β-strand	356-363	8	28
β-strand	369-373	5	28
β-strand	376-378	3	27
α-helix	381-382	2
β-strand	387-395	9	28
β-strand	402-408	7	27
β-strand	414-421	8	27
β-strand	441-444	4	32
β-strand	447-450	4	32
α-helix	451	1
β-strand	454	1	33
β-strand	462	1	33
α-helix	472-474	3
α-helix	482	1
α-helix	483-486	4
β-strand	488-491	4	34
β-strand	494-497	4	34
β-strand	507-508	2	35
β-strand	514-515	2	35
β-strand	521-522	2	36
β-strand	525-526	2	36
β-strand	533-536	4	37
β-strand	539-542	4	37
α-helix	543	1
β-strand	572-575	4	38
β-strand	578-581	4	38
α-helix	597-598	2
α-helix	599-601	3
α-helix	604-612	9
α-helix	621-624	4
β-strand	628-631	4	39
β-strand	638-643	6	39
β-strand	649-656	8	39
β-strand	663-667	5	39
β-strand	672	1	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-X	A	protein	1094	Homo sapiens	P20702 (AlphaFold model)
Integrin beta-2	B	protein	686	Homo sapiens	P05107 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4NEN_1 Integrin alpha-X (chains A)
FNLDTEELTAFRVDSAGFGDSVVQYANSWVVVGAPQKITAADQTGGLYQCGYSTGACEPI
GLQVPPEAVNMSLGLSLASTTSPSQLLACGPTVHHECGRNMYLTGLCFLLGPTQLTQRLP
VSRQECPRQEQDIVFLIDGSGSISSRNFATMMNFVRAVISQFQRPSTQFSLMQFSNKFQT
HFTFEEFRRSSNPLSLLASVHQLQGFTYTATAIQNVVHRLFHASYGARRDAAKILIVITD
GKKEGDSLDYKDVIPMADAAGIIRYAIGVGLAFQNRNSWKELNDIASKPSQEHIFKVEDF
DALKDIQNQLKEKIFAIEGTETTSSSSFELEMAQEGFSAVFTPDGPVLGAVGSFTWSGGA
FLYPPNMDPTFINMSQENVDMRDSYLGYSTELALWKGVQSLVLGAPRYQHTGKAVIFTQV
SRQWRMKAEVTGTQIGSYFGASLCSVDVDSDGSTDLVLIGAPHYYEQTRGGQVSVCPLPR
GWRRWWCDAVLYGEQGHPWGRFGAALTVLGDVNGDKLTDVVIGAPGEEENRGAVYLFHGV
LGPSISPSHSQRIAGSQLSSRLQYFGQALSGGQDLTQDGLVDLAVGARGQVLLLRTRPVL
WVGVSMQFIPAEIPRSAFECREQVVSEQTLVQSNICLYIDKRSKNLLGSRDLQSSVTLDL
ALDPGRLSPRATFQETKTRSLSRVRVLGLKAHCENFNLLLPSCVEDSVTPITLRLNFTLV
GKPLLAFRNLRPMLAADAQRYFTASLPFEKNCGADHICQDNLGISFSFPGLKSLLVGSNL
ELNAEVMVWNDGEDSYGTTITFSHPAGLSYRYVAEGQKQGQLRSLHLTCDSAPVGSQGTW
STSCRINHLIFRGGAQITFLATFDVSPKAVLGDRLLLTANVSSESNTPRTSKTTFQLELP
VKYAVYTVVSSHEQFTKYLCFSESEEKESHVAMHRYQVNNLGQRDLPVSINFWVPVELNQ
EAVWMDVEVSHPQNPSLRCSSEKIAPPASDFLAHIQKNPVLDCSIAGCLRFRCDVPSFSV
QEELDFTLKGNLSFGWVRQILQKKVSVVSVAEITFDTSVYSQLPGQEAFMRAQTTTVLEK
YKPGPAALQTLFQG

Sequence of entity 2 (B), FASTA

>4NEN_2 Integrin beta-2 (chains B)
QECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPT
SLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDD
LRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPF
AFRHVLKLTDNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRKVTRLLVFA
TDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAV
TSRMVKTYEKLTEIIPKSAVGELSEDSSNVVQLIKNAYNKLSSRVFLDHNALPDTLKVTY
DSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVL
PQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNN
SIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKC
RCHPGFEGSACQCERTTEGCLNPRRVECSGRGRCRCNVCECHSGYQLPLCQECPGCPSPC
GKYISCAECLKFEKGPFGKNCSAACPGLQLSNNPVKGRTCKERDSEGCWVAYTLEQQDGM
DRYLIYVDESRECCGGPAALQTLFQG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	5
MG	Magnesium ion	Mg	2

Water and common crystallization additives (CL) are not listed.

Primary citation

An internal ligand-bound, metastable state of a leukocyte integrin, alpha X beta 2. Sen, M., Yuki, K., Springer, T.A. J Cell Biol (2013) 203:629-642. DOI 10.1083/jcb.201308083 · PubMed

Other PDB entries of the same protein (UniProt P20702 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1N3Y 1.65 Å, Crystal structure of the alpha-X beta2 integrin I domain
4NEH 2.75 Å, An internal ligand-bound, metastable state of a leukocyte integrin, aXb2
5ES4 3.3 Å, Re-refinement of integrin ALPHAXBETA2 ectodomain in the closed/bent conformation
3K6S 3.5 Å, Structure of integrin alphaXbeta2 ectodomain
3K72 3.7 Å, Structure of integrin alphaX beta2
3K71 3.95 Å, Structure of integrin alphaX beta2 ectodomain
2LUV Structure and Binding Interface of the Cytosolic Tails of aXb2 Integrin
9ECM Structure of the human integrin alphaX transmembrane domain

Browse structure collections

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