Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6OEO

Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0002250	biological_process	adaptive immune response
A	0002331	biological_process	pre-B cell allelic exclusion
A	0003677	molecular_function	DNA binding
A	0004519	molecular_function	endonuclease activity
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0006310	biological_process	DNA recombination
A	0006325	biological_process	chromatin organization
A	0008270	molecular_function	zinc ion binding
A	0008542	biological_process	visual learning
A	0016740	molecular_function	transferase activity
A	0030183	biological_process	B cell differentiation
A	0033077	biological_process	T cell differentiation in thymus
A	0033151	biological_process	V(D)J recombination
A	0042393	molecular_function	histone binding
A	0042802	molecular_function	identical protein binding
A	0042803	molecular_function	protein homodimerization activity
A	0043029	biological_process	T cell homeostasis
A	0043565	molecular_function	sequence-specific DNA binding
A	0045580	biological_process	regulation of T cell differentiation
A	0045582	biological_process	positive regulation of T cell differentiation
A	0046872	molecular_function	metal ion binding
A	0048538	biological_process	thymus development
A	0051865	biological_process	protein autoubiquitination
A	0061630	molecular_function	ubiquitin protein ligase activity
A	0070233	biological_process	negative regulation of T cell apoptotic process
A	0070244	biological_process	negative regulation of thymocyte apoptotic process
A	2000822	biological_process	regulation of behavioral fear response
B	0002313	biological_process	mature B cell differentiation involved in immune response
B	0002326	biological_process	B cell lineage commitment
B	0002331	biological_process	pre-B cell allelic exclusion
B	0002358	biological_process	B cell homeostatic proliferation
B	0002360	biological_process	T cell lineage commitment
B	0003677	molecular_function	DNA binding
B	0003682	molecular_function	chromatin binding
B	0005515	molecular_function	protein binding
B	0005546	molecular_function	phosphatidylinositol-4,5-bisphosphate binding
B	0005547	molecular_function	phosphatidylinositol-3,4,5-trisphosphate binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0006310	biological_process	DNA recombination
B	0006325	biological_process	chromatin organization
B	0008270	molecular_function	zinc ion binding
B	0030183	biological_process	B cell differentiation
B	0030217	biological_process	T cell differentiation
B	0033077	biological_process	T cell differentiation in thymus
B	0033085	biological_process	negative regulation of T cell differentiation in thymus
B	0033151	biological_process	V(D)J recombination
B	0035064	molecular_function	methylated histone binding
B	0035091	molecular_function	phosphatidylinositol binding
B	0035265	biological_process	organ growth
B	0042742	biological_process	defense response to bacterium
B	0043325	molecular_function	phosphatidylinositol-3,4-bisphosphate binding
B	0046622	biological_process	positive regulation of organ growth
B	0046872	molecular_function	metal ion binding
B	0080025	molecular_function	phosphatidylinositol-3,5-bisphosphate binding
B	1904155	biological_process	DN2 thymocyte differentiation
C	0002250	biological_process	adaptive immune response
C	0002331	biological_process	pre-B cell allelic exclusion
C	0003677	molecular_function	DNA binding
C	0004519	molecular_function	endonuclease activity
C	0004842	molecular_function	ubiquitin-protein transferase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0006310	biological_process	DNA recombination
C	0006325	biological_process	chromatin organization
C	0008270	molecular_function	zinc ion binding
C	0008542	biological_process	visual learning
C	0016740	molecular_function	transferase activity
C	0030183	biological_process	B cell differentiation
C	0033077	biological_process	T cell differentiation in thymus
C	0033151	biological_process	V(D)J recombination
C	0042393	molecular_function	histone binding
C	0042802	molecular_function	identical protein binding
C	0042803	molecular_function	protein homodimerization activity
C	0043029	biological_process	T cell homeostasis
C	0043565	molecular_function	sequence-specific DNA binding
C	0045580	biological_process	regulation of T cell differentiation
C	0045582	biological_process	positive regulation of T cell differentiation
C	0046872	molecular_function	metal ion binding
C	0048538	biological_process	thymus development
C	0051865	biological_process	protein autoubiquitination
C	0061630	molecular_function	ubiquitin protein ligase activity
C	0070233	biological_process	negative regulation of T cell apoptotic process
C	0070244	biological_process	negative regulation of thymocyte apoptotic process
C	2000822	biological_process	regulation of behavioral fear response
D	0002313	biological_process	mature B cell differentiation involved in immune response
D	0002326	biological_process	B cell lineage commitment
D	0002331	biological_process	pre-B cell allelic exclusion
D	0002358	biological_process	B cell homeostatic proliferation
D	0002360	biological_process	T cell lineage commitment
D	0003677	molecular_function	DNA binding
D	0003682	molecular_function	chromatin binding
D	0005515	molecular_function	protein binding
D	0005546	molecular_function	phosphatidylinositol-4,5-bisphosphate binding
D	0005547	molecular_function	phosphatidylinositol-3,4,5-trisphosphate binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0006310	biological_process	DNA recombination
D	0006325	biological_process	chromatin organization
D	0008270	molecular_function	zinc ion binding
D	0030183	biological_process	B cell differentiation
D	0030217	biological_process	T cell differentiation
D	0033077	biological_process	T cell differentiation in thymus
D	0033085	biological_process	negative regulation of T cell differentiation in thymus
D	0033151	biological_process	V(D)J recombination
D	0035064	molecular_function	methylated histone binding
D	0035091	molecular_function	phosphatidylinositol binding
D	0035265	biological_process	organ growth
D	0042742	biological_process	defense response to bacterium
D	0043325	molecular_function	phosphatidylinositol-3,4-bisphosphate binding
D	0046622	biological_process	positive regulation of organ growth
D	0046872	molecular_function	metal ion binding
D	0080025	molecular_function	phosphatidylinositol-3,5-bisphosphate binding
D	1904155	biological_process	DN2 thymocyte differentiation
N	0003677	molecular_function	DNA binding
N	0005634	cellular_component	nucleus

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue CA A 1101

Chain	Residue
A	ASP600
A	ASP708
I	DA16
I	DC17

site_id	AC2
Number of Residues	3
Details	binding site for residue CA A 1102

Chain	Residue
A	ASP600
A	GLN962
I	DC17

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN A 1103

Chain	Residue
A	HIS937
A	HIS942
A	CYS727
A	CYS730

site_id	AC4
Number of Residues	4
Details	binding site for residue CA C 1101

Chain	Residue
C	ASP600
C	ASP708
J	DA16
J	DC17

site_id	AC5
Number of Residues	3
Details	binding site for residue CA C 1102

Chain	Residue
C	ASP600
C	GLN962
J	DC17

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN C 1103

Chain	Residue
C	CYS727
C	CYS730
C	HIS937
C	HIS942

Functional Information from PROSITE/UniProt

site_id	PS00353
Number of Residues	12
Details	HMG_BOX_1 HMG box A DNA-binding domain signature. FSKKCsERWKTM

Chain	Residue	Details
N	PHE41-MET52

site_id	PS00435
Number of Residues	11
Details	PEROXIDASE_1 Peroxidases proximal heme-ligand signature. DTVYILGGHSL

Chain	Residue	Details
B	ASP214-LEU224

site_id	PS00518
Number of Residues	10
Details	ZF_RING_1 Zinc finger RING-type signature. CkHlFCriCI

Chain	Residue	Details
A	CYS305-ILE314

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	70
Details	DNA_BIND: HMG box 1 => ECO:0000255\|PROSITE-ProRule:PRU00267

Chain	Residue	Details
N	PRO9-ILE79
D	TRP416-ILE484

site_id	SWS_FT_FI2
Number of Residues	68
Details	DNA_BIND: HMG box 2 => ECO:0000255\|PROSITE-ProRule:PRU00267

Chain	Residue	Details
N	PRO95-ARG163
D	CYS423
D	CYS446
D	HIS452
D	HIS455
D	CYS458
D	CYS478
D	HIS481
B	CYS423
B	CYS446
B	HIS452
B	HIS455
B	CYS458
B	CYS478
B	HIS481
D	CYS419

site_id	SWS_FT_FI3
Number of Residues	1
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P10103

Chain	Residue	Details
N	MET1
C	GLY389-GLN456

site_id	SWS_FT_FI4
Number of Residues	1
Details	SITE: Cleavage; by thrombin:thrombomodulin => ECO:0000250\|UniProtKB:P10103

Chain	Residue	Details
N	ARG10
A	CYS325
A	CYS328
C	CYS266
C	HIS270
C	CYS290
C	CYS293
C	HIS295
C	CYS305
C	HIS307
C	CYS310
A	HIS270
C	CYS313
C	CYS325
C	CYS328
A	CYS290
A	CYS293
A	HIS295
A	CYS305
A	HIS307
A	CYS310
A	CYS313

site_id	SWS_FT_FI5
Number of Residues	1
Details	SITE: Cleavage; by CASP1 => ECO:0000269\|PubMed:24474694

Chain	Residue	Details
N	ASP67
A	CYS360
A	HIS372
A	HIS376
C	CYS355
C	CYS360
C	HIS372
C	HIS376

site_id	SWS_FT_FI6
Number of Residues	8
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P10103

Chain	Residue	Details
N	LYS3
N	LYS7
N	LYS8
N	LYS12
N	LYS28
N	LYS29
N	LYS127
N	LYS128

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: Cysteine sulfonic acid (-SO3H); alternate => ECO:0000250\|UniProtKB:P63159

Chain	Residue	Details
N	CYS23
N	CYS45

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
N	LYS30
C	LYS233

site_id	SWS_FT_FI9
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
N	SER35

site_id	SWS_FT_FI10
Number of Residues	3
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P63158

Chain	Residue	Details
N	LYS43
N	LYS90
N	LYS141

site_id	SWS_FT_FI11
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18669648

Chain	Residue	Details
N	SER100

site_id	SWS_FT_FI12
Number of Residues	1
Details	MOD_RES: Cysteine sulfonic acid (-SO3H) => ECO:0000250\|UniProtKB:P63159

Chain	Residue	Details
N	CYS106

site_id	SWS_FT_FI13
Number of Residues	5
Details	CROSSLNK: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-?) => ECO:0000269\|PubMed:29618516

Chain	Residue	Details
N	LYS28
N	LYS43
N	LYS44
N	LYS68

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)