General information
PDB ID 6CG0
Title CRYO-EM STRUCTURE OF MOUSE RAG1/2 HFC COMPLEX (3.17 A)
PDB header RECOMBINATION
Date 2018-02-19
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.17
Kind dna
Organism MUS MUSCULUS, ESCHERICHIA COLI K-12, HOMO SAPIENS
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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:
pdb6cg0.pdb ACDBN FIJGLM 0
Biounits:
6cg0.pdb1.pdb ACDBN FIJGLM 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
HMG_box Domain P09429_96-138 2.6e-16 1 CL0114 N 50 138 GM  H-Bb H-Mn L-Bb 
HMG_box_2 Domain P09429_15-50 4.9e-10 1 CL0114 N 15 96 GM  H-Bb L-Bb L-Mj L-Mn 
RAG1 Family P15919_391-1008 0 1 No_clan A 395 1008 FGILM  H-Bb H-Mj H-Mn L-Bb L-Mj L-Mn 
RAG1 Family P15919_391-1008 0 1 No_clan C 392 1007 FGJLM  H-Bb H-Mj H-Mn L-Bb L-Mj L-Mn 
RAG2 Repeat P21784_51-351 9.5e-166 1 CL0186 B 51 351 I  S-Bb 
RAG2 Repeat P21784_51-351 2.4e-165 1 CL0186 D 51 351   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/C=265-1039 C DNA recombinase complex
A/C=265-1039 C endodeoxyribonuclease complex
A/C=265-1039 C nucleoplasm
A/C=265-1039 C nucleus
A/C=265-1039 F endonuclease activity
A/C=265-1039 F histone binding
A/C=265-1039 F identical protein binding
A/C=265-1039 F metal ion binding
A/C=265-1039 F protein homodimerization activity
A/C=265-1039 F sequence-specific DNA binding
A/C=265-1039 F ubiquitin protein ligase activity
A/C=265-1039 F ubiquitin-protein transferase activity
A/C=265-1039 F zinc ion binding
A/C=265-1039 P adaptive immune response
A/C=265-1039 P B cell differentiation
A/C=265-1039 P DNA recombination
A/C=265-1039 P histone monoubiquitination
A/C=265-1039 P negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
A/C=265-1039 P negative regulation of T cell apoptotic process
A/C=265-1039 P negative regulation of thymocyte apoptotic process
A/C=265-1039 P positive regulation of T cell differentiation
A/C=265-1039 P pre-B cell allelic exclusion
A/C=265-1039 P protein autoubiquitination
A/C=265-1039 P regulation of behavioral fear response
A/C=265-1039 P regulation of T cell differentiation
A/C=265-1039 P T cell differentiation in thymus
A/C=265-1039 P T cell homeostasis
A/C=265-1039 P thymus development
A/C=265-1039 P V(D)J recombination
A/C=265-1039 P visual learning
B/D=1-520 C DNA recombinase complex
B/D=1-520 C nucleoplasm
B/D=1-520 C nucleus
B/D=1-520 F chromatin binding
B/D=1-520 F methylated histone binding
B/D=1-520 F phosphatidylinositol binding
B/D=1-520 F phosphatidylinositol-3,4,5-trisphosphate binding
B/D=1-520 F phosphatidylinositol-3,4-bisphosphate binding
B/D=1-520 F phosphatidylinositol-3,5-bisphosphate binding
B/D=1-520 F phosphatidylinositol-4,5-bisphosphate binding
B/D=1-520 F sequence-specific DNA binding
B/D=1-520 F ubiquitin protein ligase activity
B/D=1-520 F zinc ion binding
B/D=1-520 P B cell differentiation
B/D=1-520 P B cell homeostatic proliferation
B/D=1-520 P B cell lineage commitment
B/D=1-520 P chromatin organization
B/D=1-520 P defense response to bacterium
B/D=1-520 P DNA recombination
B/D=1-520 P positive regulation of organ growth
B/D=1-520 P pre-B cell allelic exclusion
B/D=1-520 P T cell differentiation
B/D=1-520 P T cell differentiation in thymus
B/D=1-520 P T cell lineage commitment
B/D=1-520 P V(D)J recombination
N=15-140 C alphav-beta3 integrin-HMGB1 complex
N=15-140 C cell surface
N=15-140 C condensed chromosome
N=15-140 C cytoplasm
N=15-140 C early endosome
N=15-140 C endoplasmic reticulum-Golgi intermediate compartment
N=15-140 C extracellular region
N=15-140 C extracellular space
N=15-140 C ficolin-1-rich granule lumen
N=15-140 C neuron projection
N=15-140 C nuclear chromatin
N=15-140 C nucleoplasm
N=15-140 C nucleus
N=15-140 C secretory granule lumen
N=15-140 C transcription repressor complex
N=15-140 F bubble DNA binding
N=15-140 F C-X-C chemokine binding
N=15-140 F calcium-dependent protein kinase regulator activity
N=15-140 F chemoattractant activity
N=15-140 F chromatin binding
N=15-140 F cytokine activity
N=15-140 F damaged DNA binding
N=15-140 F DNA binding, bending
N=15-140 F DNA polymerase binding
N=15-140 F double-stranded DNA binding
N=15-140 F double-stranded RNA binding
N=15-140 F four-way junction DNA binding
N=15-140 F integrin binding
N=15-140 F lipopolysaccharide binding
N=15-140 F lyase activity
N=15-140 F phosphatidylserine binding
N=15-140 F protein kinase activator activity
N=15-140 F RAGE receptor binding
N=15-140 F repressing transcription factor binding
N=15-140 F RNA binding
N=15-140 F single-stranded DNA binding
N=15-140 F single-stranded RNA binding
N=15-140 F supercoiled DNA binding
N=15-140 F transcription coactivator activity
N=15-140 F transcription factor binding
N=15-140 F transcription regulatory region sequence-specific DNA binding
N=15-140 P activation of innate immune response
N=15-140 P apoptotic cell clearance
N=15-140 P apoptotic DNA fragmentation
N=15-140 P autophagy
N=15-140 P base-excision repair
N=15-140 P cell chemotaxis
N=15-140 P cellular response to interleukin-7
N=15-140 P cellular response to lipopolysaccharide
N=15-140 P chromatin assembly
N=15-140 P chromatin remodeling
N=15-140 P chromatin silencing
N=15-140 P dendritic cell chemotaxis
N=15-140 P developmental process
N=15-140 P DNA geometric change
N=15-140 P DNA ligation involved in DNA repair
N=15-140 P DNA recombination
N=15-140 P DNA topological change
N=15-140 P endothelial cell chemotaxis
N=15-140 P endothelial cell proliferation
N=15-140 P eye development
N=15-140 P inflammatory response
N=15-140 P inflammatory response to antigenic stimulus
N=15-140 P innate immune response
N=15-140 P lung development
N=15-140 P macrophage activation involved in immune response
N=15-140 P myeloid dendritic cell activation
N=15-140 P negative regulation of apoptotic cell clearance
N=15-140 P negative regulation of blood vessel endothelial cell migration
N=15-140 P negative regulation of CD4-positive, alpha-beta T cell differentiation
N=15-140 P negative regulation of interferon-gamma production
N=15-140 P negative regulation of RNA polymerase II transcription preinitiation complex assembly
N=15-140 P negative regulation of transcription by RNA polymerase II
N=15-140 P neuron projection development
N=15-140 P neutrophil clearance
N=15-140 P neutrophil degranulation
N=15-140 P plasmacytoid dendritic cell activation
N=15-140 P positive regulation of activated T cell proliferation
N=15-140 P positive regulation of apoptotic process
N=15-140 P positive regulation of autophagy
N=15-140 P positive regulation of blood vessel endothelial cell migration
N=15-140 P positive regulation of chemokine (C-X-C motif) ligand 2 production
N=15-140 P positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
N=15-140 P positive regulation of cytosolic calcium ion concentration
N=15-140 P positive regulation of dendritic cell differentiation
N=15-140 P positive regulation of DNA binding
N=15-140 P positive regulation of DNA ligation
N=15-140 P positive regulation of ERK1 and ERK2 cascade
N=15-140 P positive regulation of glycogen catabolic process
N=15-140 P positive regulation of innate immune response
N=15-140 P positive regulation of interferon-alpha production
N=15-140 P positive regulation of interferon-beta production
N=15-140 P positive regulation of interleukin-1 beta production
N=15-140 P positive regulation of interleukin-1 production
N=15-140 P positive regulation of interleukin-10 production
N=15-140 P positive regulation of interleukin-12 production
N=15-140 P positive regulation of interleukin-6 production
N=15-140 P positive regulation of interleukin-8 production
N=15-140 P positive regulation of JNK cascade
N=15-140 P positive regulation of MAPK cascade
N=15-140 P positive regulation of mismatch repair
N=15-140 P positive regulation of monocyte chemotactic protein-1 production
N=15-140 P positive regulation of monocyte chemotaxis
N=15-140 P positive regulation of myeloid cell differentiation
N=15-140 P positive regulation of NIK/NF-kappaB signaling
N=15-140 P positive regulation of sprouting angiogenesis
N=15-140 P positive regulation of toll-like receptor 2 signaling pathway
N=15-140 P positive regulation of toll-like receptor 4 signaling pathway
N=15-140 P positive regulation of toll-like receptor 9 signaling pathway
N=15-140 P positive regulation of transcription by RNA polymerase II
N=15-140 P positive regulation of tumor necrosis factor production
N=15-140 P positive regulation of vascular endothelial cell proliferation
N=15-140 P positive regulation of wound healing
N=15-140 P regulation of nucleotide-excision repair
N=15-140 P regulation of restriction endodeoxyribonuclease activity
N=15-140 P regulation of signaling receptor activity
N=15-140 P regulation of T cell mediated immune response to tumor cell
N=15-140 P regulation of tolerance induction
N=15-140 P regulation of transcription by RNA polymerase II
N=15-140 P regulation of transcription, DNA-templated
N=15-140 P response to glucocorticoid
N=15-140 P T-helper 1 cell activation
N=15-140 P T-helper 1 cell differentiation
N=15-140 P toll-like receptor signaling pathway
N=15-140 P tumor necrosis factor secretion
N=15-140 P V(D)J recombination
N=15-140 P viral process
Sequences
Download file with secondary structure created by Stride  
6cg0.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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L (dna): 
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M (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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N (protein): 
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