4QMG: PDB entry 4QMG

The Structure of MTDH-SND1 Complex Reveals Novel Cancer-Promoting Interactions. Determined by X-ray diffraction at 2.7 Å resolution. Released 8 Oct 2014.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,224
Mol. weight: 208.07 kDa
Ligands: CS
Released: 8 Oct 2014

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

Secondary structure: helices and β-sheets

4QMG contains 82 α-helices and 101 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: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	20-27	8	1
α-helix	29-31	3
β-strand	33-36	4	1
α-helix	44-45	2
β-strand	46-51	6	1
β-strand	54-56	3	2
α-helix	57-60	4
β-strand	61	1	3
β-strand	73	1	3
α-helix	75-76	2
α-helix	79-90	12
β-strand	94-102	9	1
β-strand	108-114	7	1
β-strand	121-122	2	1
α-helix	123-129	7
β-strand	133-135	3	2
α-helix	144-159	16
α-helix	162-164	3
α-helix	170-172	3
β-strand	177	1	4
α-helix	183-188	6
β-strand	195-204	10	4
β-strand	207-212	6	4
β-strand	217-223	7	4
β-strand	226-227	2	5
β-strand	231	1	6
β-strand	241	1	6
α-helix	242	1
α-helix	245-256	12
β-strand	260-269	10	4
β-strand	272-278	7	4
α-helix	284-291	8
β-strand	295-296	2	5
α-helix	301-303	3
α-helix	308-320	13
α-helix	324-326	3

Chain B: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	19-27	9	7
α-helix	29-31	3
β-strand	32-36	5	7
α-helix	43-45	3
β-strand	46-51	6	7
β-strand	54-56	3	8
α-helix	57-60	4
β-strand	61	1	9
β-strand	73	1	9
α-helix	74-76	3
α-helix	79-90	12
β-strand	94-102	9	7
β-strand	108-114	7	7
β-strand	121-122	2	7
α-helix	123-129	7
β-strand	133-135	3	8
α-helix	146-158	13
α-helix	162-164	3
α-helix	170-172	3
β-strand	177	1	10
α-helix	183-189	7
β-strand	195-204	10	10
β-strand	207-212	6	10
β-strand	217-223	7	10
β-strand	226-227	2	11
β-strand	231	1	12
β-strand	241	1	12
α-helix	242	1
α-helix	245-256	12
β-strand	260-269	10	10
β-strand	272-278	7	10
α-helix	284-291	8
β-strand	295-296	2	11
α-helix	308-319	12
α-helix	324-326	3

Chain C: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	20-27	8	13
α-helix	29-31	3
β-strand	33-36	4	13
α-helix	44-45	2
β-strand	46-51	6	13
β-strand	54-55	2	14
α-helix	57-60	4
β-strand	61	1	15
β-strand	73	1	15
α-helix	75-76	2
α-helix	79-90	12
β-strand	94-102	9	13
β-strand	108-114	7	13
β-strand	121-122	2	13
α-helix	123-129	7
β-strand	134-135	2	14
α-helix	141-142	2
α-helix	144-159	16
α-helix	162-164	3
α-helix	170-172	3
β-strand	177	1	16
α-helix	183-189	7
β-strand	195-204	10	16
β-strand	207-212	6	16
β-strand	217-223	7	16
β-strand	226-227	2	17
β-strand	231-232	2	18
β-strand	240-241	2	18
α-helix	242	1
α-helix	245-256	12
β-strand	260-269	10	16
β-strand	272-278	7	16
α-helix	284-290	7
β-strand	295-296	2	17
α-helix	301-303	3
α-helix	308-320	13
α-helix	324-326	3

Chain D: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	19-27	9	19
α-helix	29-31	3
β-strand	33-36	4	19
α-helix	43-45	3
β-strand	46-51	6	19
β-strand	54-55	2	20
α-helix	57-60	4
β-strand	61	1	21
α-helix	62-64	3
α-helix	72	1
β-strand	73	1	21
α-helix	74-76	3
α-helix	80-90	11
β-strand	94-102	9	19
β-strand	108-114	7	19
β-strand	121-122	2	19
α-helix	123-129	7
β-strand	134-135	2	20
α-helix	136	1
α-helix	144-158	15
α-helix	162-164	3
α-helix	170-172	3
β-strand	177	1	22
α-helix	183-188	6
β-strand	195-204	10	22
β-strand	207-212	6	22
β-strand	217-223	7	22
β-strand	226-227	2	23
β-strand	231	1	24
β-strand	241	1	24
α-helix	242	1
α-helix	245-256	12
β-strand	260-269	10	22
β-strand	272-278	7	22
α-helix	284-290	7
β-strand	295-296	2	23
α-helix	308-319	12
α-helix	324-326	3

Chain E: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	20-27	8	25
α-helix	29-31	3
β-strand	32-36	5	25
α-helix	43-45	3
β-strand	46-51	6	25
β-strand	54-56	3	26
α-helix	57-60	4
β-strand	61	1	27
β-strand	73	1	27
α-helix	75-76	2
α-helix	79-90	12
β-strand	94-101	8	25
β-strand	108-114	7	25
β-strand	121-122	2	25
α-helix	123-129	7
β-strand	133-135	3	26
α-helix	144-159	16
α-helix	162-164	3
α-helix	170-172	3
β-strand	177	1	28
α-helix	183-188	6
β-strand	195-204	10	28
β-strand	207-212	6	28
β-strand	217-223	7	28
β-strand	226-227	2	29
β-strand	231-232	2	30
β-strand	240-241	2	30
α-helix	242	1
α-helix	245-256	12
β-strand	260-269	10	28
β-strand	272-279	8	28
β-strand	282-283	2	28
α-helix	284-291	8
β-strand	295-296	2	29
α-helix	308-320	13
α-helix	324-326	3

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	395-397	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Staphylococcal nuclease domain-containing protein 1	A, B, C, D, E	protein	325	Homo sapiens	Q7KZF4 (AlphaFold model)
Protein LYRIC	F, G, H, I, J	protein	43	Homo sapiens	Q86UE4 (AlphaFold model)

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

>4QMG_1 Staphylococcal nuclease domain-containing protein 1 (chains A, B, C, D, E)
MVPTVQRGIIKMVLSGCAIIVRGQPRGGPPPERQINLSNIRAGNLARRAAATQPDAKDTP
DEPWAFPAREFLRKKLIGKEVCFTIENKTPQGREYGMIYLGKDTNGENIAESLVAEGLAT
RREGMRANNPEQNRLSECEEQAKAAKKGMWSEGNGSHTIRDLKYTIENPRHFVDSHHQKP
VNAIIEHVRDGSVVRALLLPDYYLVTVMLSGIKCPTFRREADGSETPEPFAAEAKFFTES
RLLQRDVQIILESCHNQNILGTILHPNGNITELLLKEGFARCVDWSIAVYTRGAEKLRAA
ERFAKERRLRIWRDYVAPTANLDQK

Sequence of entity 2 (F, G, H, I, J), FASTA

>4QMG_2 Protein LYRIC (chains F, G, H, I, J)
STGNASDSSSDSSSSEGDGTVSSADPNSDWNAPAEEWGNWVDE

Ligands and cofactors

ID	Name	Formula	Copies
CS	Cesium ion	Cs	5

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Structural Insights into the Tumor-Promoting Function of the MTDH-SND1 Complex. Guo, F., Wan, L., Zheng, A. et al. Cell Rep (2014) 8:1704-1713. DOI 10.1016/j.celrep.2014.08.033 · PubMed

Other PDB entries of the same protein (UniProt Q7KZF4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HQX 1.42 Å, Crystal structure of human P100 tudor domain conserved region
5M9O 1.45 Å, Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically…
3OMC 1.77 Å, Structure of human SND1 extended tudor domain in complex with the symmetrically…
3OMG 1.85 Å, Structure of human SND1 extended tudor domain in complex with the symmetrically…
3BDL 1.9 Å, Crystal structure of a truncated human Tudor-SN
2HQE 2.0 Å, Crystal structure of human P100 Tudor domain: Large fragment
2O4X 2.0 Å, Crystal structure of human P100 tudor domain
7KNW 2.65 Å, Crystal structure of SND1 in complex with C-26-A2
7KNX 2.7 Å, Crystal structure of SND1 in complex with C-26-A6
2E6N Solution structure of the TUDOR domain of Staphylococcal nuclease domain-containing…

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