4GUS: LSD2-NPAC with H3 in space group P3221

Crystal structure of LSD2-NPAC with H3 in space group P3221. Determined by X-ray diffraction at 2.23 Å resolution. Released 16 Jan 2013.

Method: X-ray diffraction
Resolution: 2.23 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,515
Mol. weight: 104.77 kDa
Ligands: ZN, FAD
Released: 16 Jan 2013

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

Secondary structure: helices and β-sheets

4GUS contains 54 α-helices and 40 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: 51 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	53	1	1
β-strand	65	1	1
β-strand	82-86	5	1
β-strand	89-92	4	1
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	2
β-strand	150-152	3	2
α-helix	153-154	2
α-helix	157-159	3
α-helix	161-166	6
α-helix	178-180	3
α-helix	184-186	3
α-helix	188-190	3
α-helix	191-196	6
α-helix	199-203	5
β-strand	211	1	3
α-helix	217-220	4
α-helix	225-228	4
β-strand	230	1	3
β-strand	272	1	4
α-helix	277	1
β-strand	278	1	5
α-helix	279	1
β-strand	284	1	4
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
α-helix	378-380	3
β-strand	384-388	5	6
α-helix	392-404	13
β-strand	407-411	5	6
β-strand	423-424	2	7
β-strand	432-433	2	7
β-strand	438-440	3	8
α-helix	446-454	9
β-strand	459-460	2	8
α-helix	461-462	2
β-strand	467-468	2	9
α-helix	469	1
α-helix	473	1
β-strand	474	1	9
α-helix	475-476	2
α-helix	477-497	21
α-helix	498-500	3
α-helix	503-505	3
β-strand	508	1	10
α-helix	509-524	16
α-helix	530-547	18
α-helix	551-553	3
β-strand	554	1	11
β-strand	555	1	10
α-helix	561-564	4
β-strand	572-574	3	8
α-helix	580-587	8
β-strand	591-593	3	6
β-strand	598-602	5	12
β-strand	608-612	5	12
β-strand	617-620	4	12
β-strand	622-625	4	6
α-helix	629-634	6
β-strand	638-640	3	12
α-helix	642-644	3
α-helix	645-653	9
β-strand	654-657	4	13
β-strand	660-665	6	9
α-helix	672-675	4
β-strand	680-683	4	9
α-helix	688-690	3
β-strand	693-699	7	9
β-strand	708-713	6	9
α-helix	716-719	4
α-helix	726-740	15
α-helix	747-749	3
β-strand	751-754	4	9
α-helix	757-759	3
β-strand	767-770	4	13
β-strand	771	1	11
α-helix	777-783	7
β-strand	786	1	6
β-strand	790-792	3	6
α-helix	795-797	3
α-helix	805-821	17

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	220-222	3

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	14-18	5
β-strand	19	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1B	A	protein	776	Homo sapiens	Q8NB78 (AlphaFold model)
Putative oxidoreductase GLYR1	B	protein	124	Homo sapiens	Q49A26 (AlphaFold model)
Histone H3.3	C	protein	21	Homo sapiens	P84243 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4GUS_1 Lysine-specific histone demethylase 1B (chains A)
PLGSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDG
YDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKT
YRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPD
CVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRP
DVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCV
QEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGI
KVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCD
LIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGI
QFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKL
AEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEK
KMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKH
SVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMA
YSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

Sequence of entity 2 (B), FASTA

>4GUS_2 Putative oxidoreductase GLYR1 (chains B)
PLGSPEFSERGSKSPLKRAQEQSPRKRGRPPKDEKDLTIPESSTVKGMMAGPMAAFKWQP
TASEPVKDADPHFHHFLLSQTEKPAVCYQAITKKLKICEEETGSTSIQAADSTAVNGSIT
PTDK

Sequence of entity 3 (C), FASTA

>4GUS_3 Histone H3.3 (chains C)
ARTMQTARKSTGGKAPRKQLA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
FAD	Flavin-adenine dinucleotide	C27 H33 N9 O15 P2	1

Water and common crystallization additives (GOL, IOD) are not listed.

Primary citation

LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Fang, R., Chen, F., Dong, Z. et al. Mol Cell (2013) 49:558-570. DOI 10.1016/j.molcel.2012.11.019 · 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
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
4GU0 3.1 Å, Crystal structure of LSD2 with H3

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