General information
PDB ID 6OER
Title CRYO-EM STRUCTURE OF MOUSE RAG1/2 NFC COMPLEX (DNA2)
PDB header RECOMBINATION/DNA
Date 2019-03-27
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.29
Kind dna
Organism MUS MUSCULUS, ESCHERICHIA COLI K-12, EQUUS CABALLUS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb6oer.pdb ABCDH FIGJ 0
Biounits:
6oer.pdb1.pdb ABCDH FIGJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
HMG_box Domain Q08IE6_99-136 2e-10 1 CL0114 H 99 136 GJ  H-Bb H-Mn L-Mn 
RAG1 Family P15919_401-1008 0 1 No_clan A 401 1008 FGIJ  H-Bb H-Mj L-Bb L-Mj L-Mn 
RAG1 Family P15919_396-1007 0 1 No_clan C 393 1008 FGIJ  H-Bb H-Mj L-Bb L-Mn 
RAG2 Repeat P21784_51-351 1.1e-169 1 CL0186 B 51 351   
RAG2 Repeat P21784_51-351 1.1e-169 1 CL0186 D 51 351 G  L-Bb 
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/C=1-1040 C DNA recombinase complex
A/C=1-1040 C endodeoxyribonuclease complex
A/C=1-1040 C nucleoplasm
A/C=1-1040 C nucleus
A/C=1-1040 F endonuclease activity
A/C=1-1040 F histone binding
A/C=1-1040 F identical protein binding
A/C=1-1040 F metal ion binding
A/C=1-1040 F protein homodimerization activity
A/C=1-1040 F sequence-specific DNA binding
A/C=1-1040 F ubiquitin protein ligase activity
A/C=1-1040 F ubiquitin-protein transferase activity
A/C=1-1040 F zinc ion binding
A/C=1-1040 P adaptive immune response
A/C=1-1040 P B cell differentiation
A/C=1-1040 P DNA recombination
A/C=1-1040 P histone monoubiquitination
A/C=1-1040 P negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
A/C=1-1040 P negative regulation of T cell apoptotic process
A/C=1-1040 P negative regulation of thymocyte apoptotic process
A/C=1-1040 P positive regulation of T cell differentiation
A/C=1-1040 P pre-B cell allelic exclusion
A/C=1-1040 P protein autoubiquitination
A/C=1-1040 P regulation of behavioral fear response
A/C=1-1040 P regulation of T cell differentiation
A/C=1-1040 P T cell differentiation in thymus
A/C=1-1040 P T cell homeostasis
A/C=1-1040 P thymus development
A/C=1-1040 P V(D)J recombination
A/C=1-1040 P visual learning
B/D=1-527 C DNA recombinase complex
B/D=1-527 C nucleoplasm
B/D=1-527 C nucleus
B/D=1-527 F chromatin binding
B/D=1-527 F methylated histone binding
B/D=1-527 F phosphatidylinositol binding
B/D=1-527 F phosphatidylinositol-3,4,5-trisphosphate binding
B/D=1-527 F phosphatidylinositol-3,4-bisphosphate binding
B/D=1-527 F phosphatidylinositol-3,5-bisphosphate binding
B/D=1-527 F phosphatidylinositol-4,5-bisphosphate binding
B/D=1-527 F sequence-specific DNA binding
B/D=1-527 F ubiquitin protein ligase activity
B/D=1-527 F zinc ion binding
B/D=1-527 P B cell differentiation
B/D=1-527 P B cell homeostatic proliferation
B/D=1-527 P B cell lineage commitment
B/D=1-527 P chromatin organization
B/D=1-527 P defense response to bacterium
B/D=1-527 P DNA recombination
B/D=1-527 P positive regulation of organ growth
B/D=1-527 P pre-B cell allelic exclusion
B/D=1-527 P T cell differentiation
B/D=1-527 P T cell differentiation in thymus
B/D=1-527 P T cell lineage commitment
B/D=1-527 P V(D)J recombination
H=1-163 C alphav-beta3 integrin-HMGB1 complex
H=1-163 C cell surface
H=1-163 C condensed chromosome
H=1-163 C cytoplasm
H=1-163 C early endosome
H=1-163 C endoplasmic reticulum-Golgi intermediate compartment
H=1-163 C extracellular space
H=1-163 C neuron projection
H=1-163 C nuclear chromatin
H=1-163 C transcription repressor complex
H=1-163 F bubble DNA binding
H=1-163 F C-X-C chemokine binding
H=1-163 F calcium-dependent protein kinase regulator activity
H=1-163 F chromatin binding
H=1-163 F cytokine activity
H=1-163 F damaged DNA binding
H=1-163 F DNA binding, bending
H=1-163 F DNA polymerase binding
H=1-163 F double-stranded RNA binding
H=1-163 F four-way junction DNA binding
H=1-163 F integrin binding
H=1-163 F lipopolysaccharide binding
H=1-163 F lyase activity
H=1-163 F non-sequence-specific DNA binding, bending
H=1-163 F phosphatidylserine binding
H=1-163 F protein kinase activator activity
H=1-163 F repressing transcription factor binding
H=1-163 F single-stranded RNA binding
H=1-163 F supercoiled DNA binding
H=1-163 F transcription coactivator activity
H=1-163 F transcription factor binding
H=1-163 F transcription regulatory region sequence-specific DNA binding
H=1-163 P activation of innate immune response
H=1-163 P autophagy
H=1-163 P base-excision repair
H=1-163 P cell chemotaxis
H=1-163 P cellular response to interleukin-7
H=1-163 P cellular response to lipopolysaccharide
H=1-163 P chromatin assembly
H=1-163 P chromatin remodeling
H=1-163 P chromatin silencing
H=1-163 P developmental process
H=1-163 P DNA geometric change
H=1-163 P DNA ligation involved in DNA repair
H=1-163 P DNA recombination
H=1-163 P endothelial cell chemotaxis
H=1-163 P endothelial cell proliferation
H=1-163 P eye development
H=1-163 P inflammatory response to antigenic stimulus
H=1-163 P innate immune response
H=1-163 P lung development
H=1-163 P macrophage activation involved in immune response
H=1-163 P myeloid dendritic cell activation
H=1-163 P negative regulation of apoptotic cell clearance
H=1-163 P negative regulation of blood vessel endothelial cell migration
H=1-163 P negative regulation of CD4-positive, alpha-beta T cell differentiation
H=1-163 P negative regulation of interferon-gamma production
H=1-163 P negative regulation of RNA polymerase II transcription preinitiation complex assembly
H=1-163 P neutrophil clearance
H=1-163 P plasmacytoid dendritic cell activation
H=1-163 P positive regulation of activated T cell proliferation
H=1-163 P positive regulation of autophagy
H=1-163 P positive regulation of blood vessel endothelial cell migration
H=1-163 P positive regulation of chemokine (C-X-C motif) ligand 2 production
H=1-163 P positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
H=1-163 P positive regulation of cytosolic calcium ion concentration
H=1-163 P positive regulation of dendritic cell differentiation
H=1-163 P positive regulation of DNA binding
H=1-163 P positive regulation of ERK1 and ERK2 cascade
H=1-163 P positive regulation of glycogen catabolic process
H=1-163 P positive regulation of innate immune response
H=1-163 P positive regulation of interferon-alpha production
H=1-163 P positive regulation of interferon-beta production
H=1-163 P positive regulation of interleukin-1 beta production
H=1-163 P positive regulation of interleukin-1 production
H=1-163 P positive regulation of interleukin-10 production
H=1-163 P positive regulation of interleukin-12 production
H=1-163 P positive regulation of interleukin-6 production
H=1-163 P positive regulation of interleukin-8 production
H=1-163 P positive regulation of JNK cascade
H=1-163 P positive regulation of mismatch repair
H=1-163 P positive regulation of monocyte chemotactic protein-1 production
H=1-163 P positive regulation of monocyte chemotaxis
H=1-163 P positive regulation of myeloid cell differentiation
H=1-163 P positive regulation of NIK/NF-kappaB signaling
H=1-163 P positive regulation of sprouting angiogenesis
H=1-163 P positive regulation of toll-like receptor 2 signaling pathway
H=1-163 P positive regulation of toll-like receptor 4 signaling pathway
H=1-163 P positive regulation of transcription by RNA polymerase II
H=1-163 P positive regulation of tumor necrosis factor production
H=1-163 P positive regulation of vascular endothelial cell proliferation
H=1-163 P positive regulation of wound healing
H=1-163 P regulation of nucleotide-excision repair
H=1-163 P regulation of restriction endodeoxyribonuclease activity
H=1-163 P regulation of signaling receptor activity
H=1-163 P regulation of T cell mediated immune response to tumor cell
H=1-163 P regulation of tolerance induction
H=1-163 P regulation of transcription by RNA polymerase II
H=1-163 P regulation of transcription, DNA-templated
H=1-163 P response to glucocorticoid
H=1-163 P T-helper 1 cell activation
H=1-163 P T-helper 1 cell differentiation
H=1-163 P tumor necrosis factor secretion
H=1-163 P V(D)J recombination
Sequences
Download file with secondary structure created by Stride  
6oer.pdb1.pdb:   [ download sequences in FASTA format ]
F (dna): 
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G (dna): 
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I (dna): 
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J (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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H (protein): 
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