6PWV

Cryo-EM structure of MLL1 core complex bound to the nucleosome

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000976	molecular_function	transcription cis-regulatory region binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005730	cellular_component	nucleolus
A	0006325	biological_process	chromatin organization
A	0006974	biological_process	DNA damage response
A	0035097	cellular_component	histone methyltransferase complex
A	0042393	molecular_function	histone binding
A	0043627	biological_process	response to estrogen
A	0044665	cellular_component	MLL1/2 complex
A	0044666	cellular_component	MLL3/4 complex
A	0045815	biological_process	transcription initiation-coupled chromatin remodeling
A	0048188	cellular_component	Set1C/COMPASS complex
A	0071339	cellular_component	MLL1 complex
B	0000122	biological_process	negative regulation of transcription by RNA polymerase II
B	0000123	cellular_component	histone acetyltransferase complex
B	0001501	biological_process	skeletal system development
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0006094	biological_process	gluconeogenesis
B	0006325	biological_process	chromatin organization
B	0006355	biological_process	regulation of DNA-templated transcription
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0035064	molecular_function	methylated histone binding
B	0035097	cellular_component	histone methyltransferase complex
B	0042393	molecular_function	histone binding
B	0042800	molecular_function	histone H3K4 methyltransferase activity
B	0044545	cellular_component	NSL complex
B	0044665	cellular_component	MLL1/2 complex
B	0044666	cellular_component	MLL3/4 complex
B	0045722	biological_process	positive regulation of gluconeogenesis
B	0045815	biological_process	transcription initiation-coupled chromatin remodeling
B	0045893	biological_process	positive regulation of DNA-templated transcription
B	0045995	biological_process	regulation of embryonic development
B	0048188	cellular_component	Set1C/COMPASS complex
B	0051302	biological_process	regulation of cell division
B	0051726	biological_process	regulation of cell cycle
B	0071339	cellular_component	MLL1 complex
B	0072686	cellular_component	mitotic spindle
B	0090043	biological_process	regulation of tubulin deacetylation
B	0140672	cellular_component	ATAC complex
D	0048188	cellular_component	Set1C/COMPASS complex
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005794	cellular_component	Golgi apparatus
E	0005802	cellular_component	trans-Golgi network
E	0006325	biological_process	chromatin organization
E	0016197	biological_process	endosomal transport
E	0035097	cellular_component	histone methyltransferase complex
E	0042802	molecular_function	identical protein binding
E	0042803	molecular_function	protein homodimerization activity
E	0044665	cellular_component	MLL1/2 complex
E	0044666	cellular_component	MLL3/4 complex
E	0045815	biological_process	transcription initiation-coupled chromatin remodeling
E	0048188	cellular_component	Set1C/COMPASS complex
E	0071339	cellular_component	MLL1 complex
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005794	cellular_component	Golgi apparatus
F	0005802	cellular_component	trans-Golgi network
F	0006325	biological_process	chromatin organization
F	0016197	biological_process	endosomal transport
F	0035097	cellular_component	histone methyltransferase complex
F	0042802	molecular_function	identical protein binding
F	0042803	molecular_function	protein homodimerization activity
F	0044665	cellular_component	MLL1/2 complex
F	0044666	cellular_component	MLL3/4 complex
F	0045815	biological_process	transcription initiation-coupled chromatin remodeling
F	0048188	cellular_component	Set1C/COMPASS complex
F	0071339	cellular_component	MLL1 complex
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005694	cellular_component	chromosome
G	0030527	molecular_function	structural constituent of chromatin
G	0046982	molecular_function	protein heterodimerization activity
H	0000786	cellular_component	nucleosome
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005694	cellular_component	chromosome
H	0006334	biological_process	nucleosome assembly
H	0030527	molecular_function	structural constituent of chromatin
H	0046982	molecular_function	protein heterodimerization activity
I	0000786	cellular_component	nucleosome
I	0003677	molecular_function	DNA binding
I	0005634	cellular_component	nucleus
I	0005694	cellular_component	chromosome
I	0030527	molecular_function	structural constituent of chromatin
I	0046982	molecular_function	protein heterodimerization activity
J	0000786	cellular_component	nucleosome
J	0003677	molecular_function	DNA binding
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005694	cellular_component	chromosome
J	0030527	molecular_function	structural constituent of chromatin
J	0046982	molecular_function	protein heterodimerization activity
K	0000786	cellular_component	nucleosome
K	0003677	molecular_function	DNA binding
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005694	cellular_component	chromosome
K	0030527	molecular_function	structural constituent of chromatin
K	0046982	molecular_function	protein heterodimerization activity
L	0000786	cellular_component	nucleosome
L	0003677	molecular_function	DNA binding
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005694	cellular_component	chromosome
L	0006334	biological_process	nucleosome assembly
L	0030527	molecular_function	structural constituent of chromatin
L	0046982	molecular_function	protein heterodimerization activity
M	0000786	cellular_component	nucleosome
M	0003677	molecular_function	DNA binding
M	0005634	cellular_component	nucleus
M	0005694	cellular_component	chromosome
M	0030527	molecular_function	structural constituent of chromatin
M	0046982	molecular_function	protein heterodimerization activity
N	0000786	cellular_component	nucleosome
N	0003677	molecular_function	DNA binding
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0005694	cellular_component	chromosome
N	0030527	molecular_function	structural constituent of chromatin
N	0046982	molecular_function	protein heterodimerization activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	binding site for residue SAH C 4001

Chain	Residue
C	ILE3838
C	HIS3839
C	GLY3840
C	ARG3841
C	TYR3883
C	PRO3956
C	CYS3957
C	ASN3958
C	SAH4003

---

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN C 4002

Chain	Residue
C	CYS3909
C	CYS3959
C	CYS3964
C	ZN4004

---

site_id	AC3
Number of Residues	12
Details	binding site for residue SAH C 4003

Chain	Residue
C	ARG3841
C	TYR3883
C	ARG3903
C	PHE3904
C	ILE3905
C	ASN3906
C	HIS3907
C	TYR3944
C	PRO3956
C	CYS3957
C	LEU3968
C	SAH4001

---

site_id	AC4
Number of Residues	6
Details	binding site for residue ZN C 4004

Chain	Residue
C	HIS3907
C	SER3908
C	CYS3909
C	CYS3957
C	CYS3959
C	ZN4002

---

Functional Information from PROSITE/UniProt

site_id	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
I	ALA21-VAL27

---

site_id	PS00047
Number of Residues	5
Details	HISTONE_H4 Histone H4 signature. GAKRH

Chain	Residue	Details
H	GLY14-HIS18

---

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
G	LYS14-LEU20

---

site_id	PS00357
Number of Residues	23
Details	HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
J	ARG89-GLY111

---

site_id	PS00678
Number of Residues	15
Details	WD_REPEATS_1 Trp-Asp (WD) repeats signature. LVSAsdDkTLKIWDV

Chain	Residue	Details
B	LEU102-VAL116
B	ILE144-VAL158
B	ILE186-THR200
B	ILE274-LEU288

---

site_id	PS00959
Number of Residues	9
Details	HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI

Chain	Residue	Details
G	PRO66-ILE74

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	33
Details	ZN_FING: C4-type

Chain	Residue	Details
D	ARG117-SER150
F	MET1
J	LYS12
J	LYS17
N	LYS2
N	LYS9
N	LYS12
N	LYS17

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231

Chain	Residue	Details
D	LYS101
F	SER19

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Asymmetric dimethylarginine; by PRMT1 and PRMT5 => ECO:0000269|PubMed:21285357

Chain	Residue	Details
D	PRO296
F	LYS35
M	LYS9
M	LYS95

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
D	VAL316
M	LYS36
F	LYS35

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8

Chain	Residue	Details
I	LYS74
I	LYS75
M	LYS74
M	LYS75
L	LYS8
L	LYS16
L	LYS44
L	LYS79

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: N5-methylglutamine => ECO:0000250

Chain	Residue	Details
I	GLN104
M	GLN104
L	LYS12
L	LYS20

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8

Chain	Residue	Details
I	LYS118
M	LYS118
L	LYS31
L	LYS91

---

site_id	SWS_FT_FI8
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250

Chain	Residue	Details
I	LYS13
L	SER47
I	LYS15
I	LYS119
M	LYS13
M	LYS15
M	LYS119

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805

Chain	Residue	Details
H	TYR51
H	TYR88
L	TYR51
L	TYR88

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805

Chain	Residue	Details
H	LYS59
K	LYS64
L	LYS59
G	LYS27
G	LYS36
G	LYS64
K	LYS18
K	LYS23
K	LYS27
K	LYS36

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805

Chain	Residue	Details
H	LYS77
L	LYS77

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805

Chain	Residue	Details
H	LYS31
L	LYS31

---

site_id	SWS_FT_FI13
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P62805

Chain	Residue	Details
G	LYS37
H	LYS91
L	LYS91

---

site_id	SWS_FT_FI14
Number of Residues	2
Details	MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
G	TYR41
K	TYR41

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228

Chain	Residue	Details
G	LYS56
G	LYS79
K	LYS56
K	LYS79

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
G	SER57
K	SER57

---

site_id	SWS_FT_FI17
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
G	THR80
G	THR107
K	THR80
K	THR107

---

site_id	SWS_FT_FI18
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243

Chain	Residue	Details
G	SER86
K	SER86

---

site_id	SWS_FT_FI19
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
G	LYS115
K	LYS115

---

site_id	SWS_FT_FI20
Number of Residues	2
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
G	LYS122
K	LYS122

---

site_id	SWS_FT_FI21
Number of Residues	2
Details	LIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
G	CYS110
K	CYS110

---