4GU0: LSD2 with H3

Crystal structure of LSD2 with H3. Determined by X-ray diffraction at 3.1 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 24,156
Mol. weight: 357.72 kDa
Ligands: FAD, ZN
Released: 13 Feb 2013

Explore 4GU0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GU0 contains 168 α-helices and 156 β-strands across 6 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: 40 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	65	1	1
β-strand	83-84	2	1
β-strand	90-91	2	1
α-helix	93-100	8
α-helix	107-118	12
α-helix	124-125	2
α-helix	127-130	4
α-helix	131-135	5
α-helix	137-138	2
β-strand	139-141	3	2
β-strand	150-152	3	2
α-helix	153-154	2
α-helix	161-166	6
α-helix	188-190	3
α-helix	192-195	4
α-helix	200-203	4
β-strand	211	1	3
α-helix	217-220	4
α-helix	225-227	3
β-strand	230	1	3
β-strand	272	1	4
β-strand	284	1	4
α-helix	291-296	6
α-helix	298-300	3
α-helix	305-318	14
α-helix	328-331	4
α-helix	332-334	3
α-helix	341-359	19
α-helix	378-380	3
β-strand	384-388	5	5
α-helix	392-404	13
β-strand	407-411	5	5
β-strand	423-427	5	6
β-strand	430-433	4	6
β-strand	438-439	2	7
α-helix	446-452	7
β-strand	459-460	2	7
α-helix	461-462	2
β-strand	467-468	2	8
β-strand	474	1	8
α-helix	477-497	21
α-helix	503-505	3
β-strand	508	1	9
α-helix	509-523	15
α-helix	530-547	18
β-strand	554	1	10
β-strand	555	1	9
α-helix	561-564	4
α-helix	566-567	2
β-strand	573-574	2	7
α-helix	579-586	8
β-strand	591-593	3	5
β-strand	598-602	5	11
β-strand	608-612	5	11
β-strand	617-620	4	11
β-strand	622-625	4	5
α-helix	629-633	5
β-strand	638-640	3	11
α-helix	642-644	3
α-helix	645-652	8
β-strand	654-655	2	12
β-strand	659-665	7	8
α-helix	672-675	4
β-strand	680-683	4	8
β-strand	693-699	7	8
β-strand	708-714	7	8
α-helix	715-718	4
α-helix	726-740	15
α-helix	745-749	5
β-strand	751-754	4	8
β-strand	769-770	2	12
β-strand	771	1	10
α-helix	777-783	7
β-strand	786	1	5
β-strand	790-792	3	5
α-helix	795-797	3
α-helix	805-821	17

Chain B: 39 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	65	1	13
β-strand	83-86	4	13
β-strand	89-91	3	13
α-helix	93-100	8
α-helix	107-120	14
α-helix	124-125	2
α-helix	127-130	4
α-helix	131-135	5
β-strand	139-141	3	14
β-strand	150-152	3	14
α-helix	153-154	2
α-helix	161-166	6
α-helix	188-190	3
α-helix	192-195	4
α-helix	199-204	6
β-strand	211	1	15
α-helix	218-220	3
β-strand	223	1	16
α-helix	225-227	3
β-strand	230	1	15
β-strand	272	1	17
β-strand	278	1	18
β-strand	280	1	19
β-strand	284	1	17
α-helix	291-296	6
α-helix	298-300	3
α-helix	305-320	16
α-helix	328-331	4
α-helix	332-334	3
α-helix	341-359	19
β-strand	384-388	5	20
α-helix	392-404	13
β-strand	407-411	5	20
β-strand	423-424	2	21
β-strand	432-433	2	21
β-strand	438-439	2	22
α-helix	446-452	7
β-strand	459-460	2	22
α-helix	461-462	2
β-strand	467-468	2	23
α-helix	469	1
β-strand	474	1	23
α-helix	477-498	22
α-helix	503-505	3
β-strand	508	1	24
α-helix	509-523	15
α-helix	530-547	18
α-helix	551-553	3
β-strand	554	1	25
β-strand	555	1	24
α-helix	561-564	4
β-strand	567	1	19
β-strand	573-574	2	22
α-helix	579-587	9
β-strand	591-593	3	20
β-strand	598-602	5	26
β-strand	608-612	5	26
β-strand	617-620	4	26
β-strand	622-625	4	20
α-helix	629-633	5
β-strand	638-640	3	26
α-helix	642-644	3
α-helix	645-651	7
β-strand	654-655	2	27
β-strand	659-665	7	23
α-helix	672-675	4
β-strand	680-683	4	23
β-strand	693-699	7	23
β-strand	708-714	7	23
α-helix	716-720	5
α-helix	726-740	15
α-helix	747-749	3
β-strand	751-754	4	23
β-strand	769-770	2	27
β-strand	771	1	25
α-helix	777-782	6
β-strand	786	1	20
β-strand	790-792	3	20
α-helix	795-797	3
α-helix	805-820	16

Chain C: 43 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	65	1	28
β-strand	83-86	4	28
β-strand	89-91	3	28
α-helix	93-100	8
α-helix	107-120	14
α-helix	124-125	2
α-helix	127-130	4
α-helix	131-135	5
α-helix	137-138	2
β-strand	139-141	3	29
β-strand	150-152	3	29
α-helix	153-154	2
α-helix	161-166	6
α-helix	184-186	3
α-helix	188-190	3
α-helix	191-195	5
α-helix	199-203	5
β-strand	211	1	30
α-helix	217-219	3
α-helix	225-228	4
β-strand	230	1	30
β-strand	272	1	31
β-strand	284	1	31
α-helix	291-296	6
α-helix	298-300	3
α-helix	305-318	14
α-helix	328-330	3
α-helix	332-334	3
α-helix	341-359	19
β-strand	384-388	5	32
α-helix	392-404	13
β-strand	407-411	5	32
β-strand	423-424	2	33
β-strand	432-433	2	33
β-strand	438-440	3	34
α-helix	446-453	8
β-strand	459-460	2	34
α-helix	461-462	2
β-strand	467-468	2	35
α-helix	469	1
β-strand	474	1	35
α-helix	475-476	2
α-helix	477-497	21
α-helix	503-505	3
β-strand	508	1	36
α-helix	509-524	16
α-helix	530-547	18
β-strand	554	1	37
β-strand	555	1	36
α-helix	561-564	4
β-strand	572-574	3	34
α-helix	579-587	9
β-strand	592-593	2	32
β-strand	598-602	5	38
β-strand	608-612	5	38
β-strand	617-620	4	38
β-strand	622-625	4	32
α-helix	629-634	6
β-strand	638-640	3	38
α-helix	642-644	3
α-helix	645-653	9
β-strand	654-657	4	39
β-strand	660-665	6	35
α-helix	672-675	4
β-strand	680-683	4	35
α-helix	689-691	3
β-strand	693-699	7	35
β-strand	708-713	6	35
α-helix	716-719	4
α-helix	726-740	15
α-helix	747-749	3
β-strand	751-754	4	35
α-helix	757-759	3
β-strand	767-770	4	39
β-strand	771	1	37
α-helix	778-782	5
β-strand	786	1	32
β-strand	790-792	3	32
α-helix	795-797	3
α-helix	805-819	15

Chain D: 42 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	65	1	40
β-strand	83-86	4	40
β-strand	89-91	3	40
α-helix	93-100	8
α-helix	107-118	12
α-helix	124-125	2
α-helix	127-130	4
α-helix	131-135	5
α-helix	137-138	2
β-strand	139-141	3	41
β-strand	150-152	3	41
α-helix	153-154	2
α-helix	161-166	6
α-helix	188-190	3
α-helix	192-195	4
α-helix	200-203	4
β-strand	211	1	42
β-strand	212	1	43
α-helix	218-220	3
α-helix	225-228	4
β-strand	230	1	42
β-strand	272	1	44
β-strand	284	1	44
α-helix	291-296	6
α-helix	298-300	3
α-helix	304-320	17
α-helix	328-331	4
α-helix	332-334	3
β-strand	336	1	43
α-helix	341-359	19
α-helix	378-380	3
β-strand	384-388	5	45
α-helix	392-404	13
β-strand	407-411	5	45
β-strand	423-424	2	46
β-strand	432-433	2	46
β-strand	438-440	3	47
α-helix	446-453	8
β-strand	459-460	2	47
α-helix	461-462	2
β-strand	467-468	2	48
α-helix	473	1
β-strand	474	1	48
α-helix	475-476	2
α-helix	477-498	22
α-helix	503-505	3
β-strand	508	1	49
α-helix	509-523	15
α-helix	530-547	18
β-strand	554	1	50
β-strand	555	1	49
α-helix	561-564	4
β-strand	572-574	3	47
α-helix	579-586	8
β-strand	592-593	2	45
β-strand	598-602	5	51
β-strand	608-612	5	51
β-strand	617-620	4	51
β-strand	622-625	4	45
α-helix	629-634	6
β-strand	638-640	3	51
α-helix	642-644	3
α-helix	645-653	9
β-strand	654-657	4	52
β-strand	660-665	6	48
α-helix	672-675	4
β-strand	680-683	4	48
β-strand	693-699	7	48
β-strand	708-713	6	48
α-helix	716-719	4
α-helix	726-740	15
α-helix	747-749	3
β-strand	751-754	4	48
α-helix	757-759	3
β-strand	767-770	4	52
β-strand	771	1	50
α-helix	777-783	7
β-strand	786	1	45
β-strand	790-792	3	45
α-helix	795-797	3
α-helix	805-819	15

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	14-17	4

Chain F: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	14-17	4
β-strand	19	1	18
β-strand	25	1	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1B	A, B, C, D	protein	776	Homo sapiens	Q8NB78 (AlphaFold model)
Histone H3.3	E, F	protein	26	Homo sapiens	P84243 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4GU0_1 Lysine-specific histone demethylase 1B (chains A, B, C, D)
PLGSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDG
YDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKT
YRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPD
CVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRP
DVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCV
QEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGI
KVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCD
LIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGI
QFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKL
AEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEK
KMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKH
SVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMA
YSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

Sequence of entity 2 (E, F), FASTA

>4GU0_2 Histone H3.3 (chains E, F)
ARTMQTARKSTGGKAPRKQLATKAAR

Ligands and cofactors

ID	Name	Formula	Copies
FAD	Flavin-adenine dinucleotide	C27 H33 N9 O15 P2	4
ZN	Zinc ion	Zn	12

Primary citation

Structural insight into substrate recognition by histone demethylase LSD2/KDM1b. Chen, F., Yang, H., Dong, Z. et al. Cell Res (2013) 23:306-309. DOI 10.1038/cr.2013.17 · PubMed

Other PDB entries of the same protein (UniProt Q8NB78 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HSU 1.99 Å, Crystal structure of LSD2-NPAC with H3(1-26)in space group P21
4GUT 2.0 Å, Crystal structure of LSD2-NPAC
7XE2 2.05 Å, Crystal structure of LSD2 in complex with trans-4-Br-PCPA
7XE1 2.07 Å, Crystal structure of LSD2 in complex with cis-4-Br-PCPA
4FWE 2.13 Å, Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A
4GUS 2.23 Å, Crystal structure of LSD2-NPAC with H3 in space group P3221
4GUU 2.3 Å, Crystal structure of LSD2-NPAC with tranylcypromine
4GUR 2.51 Å, Crystal structure of LSD2-NPAC with H3 in space group P21
4FWF 2.7 Å, Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic
7XE3 2.82 Å, Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024)
4FWJ 2.9 Å, Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A
4GU1 2.94 Å, Crystal structure of LSD2

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