4NEH: Integrin alpha-X

An internal ligand-bound, metastable state of a leukocyte integrin, aXb2. Determined by X-ray diffraction at 2.75 Å resolution. Released 15 Jan 2014.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 2
Atoms: 14,175
Mol. weight: 200.25 kDa
Ligands: CA, MG, NAG
Released: 15 Jan 2014

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

Secondary structure: helices and β-sheets

4NEH contains 67 α-helices and 145 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: 38 helices, 94 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	46-50	5	3
β-strand	57-59	3	3
α-helix	60-61	2
β-strand	69	1	5
β-strand	73	1	4
β-strand	76-81	6	5
β-strand	84-97	14	5
β-strand	100-110	11	5
β-strand	117-119	3	5
α-helix	123-127	5
β-strand	128	1	6
α-helix	129-130	2
β-strand	131-138	8	7
α-helix	146-160	15
β-strand	167-174	8	7
β-strand	178-182	5	7
α-helix	184-188	5
α-helix	193-195	3
β-strand	207	1	8
α-helix	209-219	11
α-helix	223-225	3
β-strand	232-239	8	7
β-strand	244-245	2	8
α-helix	250-259	10
β-strand	262-268	7	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	302-306	5
β-strand	310	1	6
α-helix	311-314	4
β-strand	315	1	9
α-helix	317-319	3
α-helix	325	1
β-strand	326	1	9
α-helix	327-328	2
β-strand	335-342	8	10
β-strand	345-350	6	10
α-helix	353-356	4
β-strand	360-362	3	10
β-strand	370-372	3	10
α-helix	379-381	3
β-strand	389-394	6	11
β-strand	399-405	7	11
α-helix	408-410	3
β-strand	413-420	8	11
β-strand	423-431	9	11
β-strand	442-446	5	12
β-strand	456-465	10	12
β-strand	470	1	12
β-strand	471	1	13
β-strand	472-477	6	12
α-helix	478-480	3
α-helix	483-485	3
β-strand	489-491	3	12
β-strand	502	1	13
β-strand	505-510	6	14
β-strand	519-524	6	14
α-helix	527-530	4
β-strand	532	1	15
β-strand	533-537	5	14
β-strand	539-540	2	16
β-strand	544-545	2	16
β-strand	551-554	4	14
α-helix	555-558	4
β-strand	565	1	15
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	17
β-strand	613	1	18
α-helix	627-628	2
β-strand	629-641	13	17
β-strand	654-662	9	19
β-strand	672-673	2	17
β-strand	680-687	8	19
β-strand	690-700	11	17
α-helix	710	1
β-strand	711-721	11	19
α-helix	722-723	2
β-strand	724	1	20
α-helix	725-727	3
β-strand	730	1	20
β-strand	733-734	2	17
β-strand	741-746	6	19
α-helix	747	1
β-strand	748	1	18
α-helix	749-750	2
β-strand	751	1	21
β-strand	757	1	21
β-strand	763-767	5	22
β-strand	774-776	3	23
β-strand	781-789	9	22
β-strand	795-805	11	24
β-strand	808-810	3	22
β-strand	828-834	7	24
β-strand	839-848	10	24
β-strand	849	1	25
β-strand	850-851	2	24
β-strand	856-865	10	22
α-helix	866	1
β-strand	874-882	9	24
β-strand	895-900	6	24
β-strand	901-905	5	23
β-strand	907-911	5	26
β-strand	918-922	5	27
β-strand	929-940	12	26
β-strand	946-958	13	27
β-strand	961-962	2	27
β-strand	964-970	7	26
β-strand	980-984	5	27
α-helix	985-988	4
α-helix	991-997	7
β-strand	1000-1001	2	27
β-strand	1007-1018	12	27
β-strand	1023-1033	11	26
α-helix	1035-1039	5
β-strand	1044-1054	11	27
β-strand	1060-1062	3	23
α-helix	1063	1
α-helix	1067-1070	4
β-strand	1071-1081	11	27

Chain B: 29 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	22-24	3	28
α-helix	37-39	3
β-strand	40-41	2	28
α-helix	47-49	3
β-strand	56-57	2	28
β-strand	62-65	4	29
β-strand	76-77	2	30
β-strand	80-85	6	29
β-strand	86	1	31
β-strand	89	1	31
β-strand	91-97	7	30
β-strand	99	1	32
β-strand	105-112	8	33
α-helix	115-117	3
α-helix	124-138	15
β-strand	142-149	8	33
α-helix	162-166	5
β-strand	176	1	34
β-strand	182-189	8	33
α-helix	192-200	9
β-strand	204	1	34
β-strand	212	1	35
α-helix	214-223	10
α-helix	225-228	4
β-strand	234-241	8	33
β-strand	245	1	35
α-helix	250-254	5
α-helix	258-260	3
β-strand	270	1	33
α-helix	272-275	4
α-helix	278-281	4
α-helix	282-291	10
β-strand	294-301	8	33
α-helix	302-304	3
α-helix	305-309	5
α-helix	311-314	4
β-strand	319-323	5	33
α-helix	330-342	13
β-strand	345-349	5	29
β-strand	356-363	8	30
β-strand	369-373	5	30
β-strand	376-378	3	29
α-helix	381-382	2
β-strand	383	1	32
β-strand	387-395	9	30
β-strand	402-408	7	29
β-strand	414-421	8	29
α-helix	441	1
β-strand	442-444	3	36
β-strand	447-449	3	36
β-strand	454-455	2	37
β-strand	461-462	2	37
β-strand	481	1	25
α-helix	482	1
α-helix	483-486	4
β-strand	488-491	4	38
β-strand	494-497	4	38
β-strand	508	1	39
β-strand	514	1	39
β-strand	521-522	2	40
β-strand	525-526	2	40
α-helix	529-532	4
β-strand	533-536	4	41
β-strand	539-542	4	41
α-helix	543	1
β-strand	546-547	2	42
β-strand	553-554	2	42
β-strand	572-575	4	43
β-strand	578-581	4	43
α-helix	596-598	3
α-helix	600-602	3
α-helix	604-612	9
α-helix	615-617	3
α-helix	621-624	4
β-strand	628-631	4	44
β-strand	638-643	6	44
β-strand	649-657	9	44
β-strand	662-667	6	44
β-strand	672	1	44

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

>4NEH_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

>4NEH_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
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (CL, NA) 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
4NEN 2.9 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

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