General information
PDB ID 6CIM
Title PRE-REACTION COMPLEX, RAG1(E962Q)/2-NICKED/INTACT 12/23RSS COMPLEX IN MN2+
PDB header RECOMBINATION/DNA
Date 2018-02-24
Experimental method X-RAY DIFFRACTION
Resolution (A) 3.6
Kind dna
Organism MUS MUSCULUS, 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:
pdb6cim.pdb ABCDN FILGJ 0
Biounits:
6cim.pdb1.pdb ABCDN FILGJ 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_95-158 2.2e-22 1 CL0114 N 47 159 GJ  H-Bb H-Mj H-Mn 
HMG_box_2 Domain P09429_15-50 2e-05 1 CL0114 N 19 48 GJ  H-Bb H-Mn 
RAG1 Family P15919_396-1007 0 1 No_clan A 395 1007 FGJL  H-Bb H-Mj L-Bb 
RAG1 Family P15919_396-1007 0 1 No_clan C 396 1007 FGJL  H-Bb H-Mj L-Bb L-Mn 
RAG2 Repeat P21784_51-351 1.4e-164 1 CL0186 B 51 350 F   
RAG2 Repeat P21784_51-351 3e-162 1 CL0186 D 51 351   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/C=384-1008 C DNA recombinase complex
A/C=384-1008 C endodeoxyribonuclease complex
A/C=384-1008 C nucleoplasm
A/C=384-1008 C nucleus
A/C=384-1008 F endonuclease activity
A/C=384-1008 F histone binding
A/C=384-1008 F identical protein binding
A/C=384-1008 F metal ion binding
A/C=384-1008 F protein homodimerization activity
A/C=384-1008 F sequence-specific DNA binding
A/C=384-1008 F ubiquitin protein ligase activity
A/C=384-1008 F ubiquitin-protein transferase activity
A/C=384-1008 F zinc ion binding
A/C=384-1008 P adaptive immune response
A/C=384-1008 P B cell differentiation
A/C=384-1008 P DNA recombination
A/C=384-1008 P histone monoubiquitination
A/C=384-1008 P negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
A/C=384-1008 P negative regulation of T cell apoptotic process
A/C=384-1008 P negative regulation of thymocyte apoptotic process
A/C=384-1008 P positive regulation of T cell differentiation
A/C=384-1008 P pre-B cell allelic exclusion
A/C=384-1008 P protein autoubiquitination
A/C=384-1008 P regulation of behavioral fear response
A/C=384-1008 P regulation of T cell differentiation
A/C=384-1008 P T cell differentiation in thymus
A/C=384-1008 P T cell homeostasis
A/C=384-1008 P thymus development
A/C=384-1008 P V(D)J recombination
A/C=384-1008 P visual learning
B/D=1-359 C DNA recombinase complex
B/D=1-359 C nucleoplasm
B/D=1-359 C nucleus
B/D=1-359 F chromatin binding
B/D=1-359 F methylated histone binding
B/D=1-359 F phosphatidylinositol binding
B/D=1-359 F phosphatidylinositol-3,4,5-trisphosphate binding
B/D=1-359 F phosphatidylinositol-3,4-bisphosphate binding
B/D=1-359 F phosphatidylinositol-3,5-bisphosphate binding
B/D=1-359 F phosphatidylinositol-4,5-bisphosphate binding
B/D=1-359 F sequence-specific DNA binding
B/D=1-359 F ubiquitin protein ligase activity
B/D=1-359 F zinc ion binding
B/D=1-359 P B cell differentiation
B/D=1-359 P B cell homeostatic proliferation
B/D=1-359 P B cell lineage commitment
B/D=1-359 P chromatin organization
B/D=1-359 P defense response to bacterium
B/D=1-359 P DNA recombination
B/D=1-359 P positive regulation of organ growth
B/D=1-359 P pre-B cell allelic exclusion
B/D=1-359 P T cell differentiation
B/D=1-359 P T cell differentiation in thymus
B/D=1-359 P T cell lineage commitment
B/D=1-359 P V(D)J recombination
N=1-163 C alphav-beta3 integrin-HMGB1 complex
N=1-163 C cell surface
N=1-163 C condensed chromosome
N=1-163 C cytoplasm
N=1-163 C early endosome
N=1-163 C endoplasmic reticulum-Golgi intermediate compartment
N=1-163 C extracellular region
N=1-163 C extracellular space
N=1-163 C ficolin-1-rich granule lumen
N=1-163 C neuron projection
N=1-163 C nuclear chromatin
N=1-163 C nucleoplasm
N=1-163 C nucleus
N=1-163 C secretory granule lumen
N=1-163 C transcription repressor complex
N=1-163 F bubble DNA binding
N=1-163 F C-X-C chemokine binding
N=1-163 F calcium-dependent protein kinase regulator activity
N=1-163 F chemoattractant activity
N=1-163 F chromatin binding
N=1-163 F cytokine activity
N=1-163 F damaged DNA binding
N=1-163 F DNA binding, bending
N=1-163 F DNA polymerase binding
N=1-163 F double-stranded DNA binding
N=1-163 F double-stranded RNA binding
N=1-163 F four-way junction DNA binding
N=1-163 F integrin binding
N=1-163 F lipopolysaccharide binding
N=1-163 F lyase activity
N=1-163 F phosphatidylserine binding
N=1-163 F protein kinase activator activity
N=1-163 F RAGE receptor binding
N=1-163 F repressing transcription factor binding
N=1-163 F RNA binding
N=1-163 F single-stranded DNA binding
N=1-163 F single-stranded RNA binding
N=1-163 F supercoiled DNA binding
N=1-163 F transcription coactivator activity
N=1-163 F transcription factor binding
N=1-163 F transcription regulatory region sequence-specific DNA binding
N=1-163 P activation of innate immune response
N=1-163 P apoptotic cell clearance
N=1-163 P apoptotic DNA fragmentation
N=1-163 P autophagy
N=1-163 P base-excision repair
N=1-163 P cell chemotaxis
N=1-163 P cellular response to interleukin-7
N=1-163 P cellular response to lipopolysaccharide
N=1-163 P chromatin assembly
N=1-163 P chromatin remodeling
N=1-163 P chromatin silencing
N=1-163 P dendritic cell chemotaxis
N=1-163 P developmental process
N=1-163 P DNA geometric change
N=1-163 P DNA ligation involved in DNA repair
N=1-163 P DNA recombination
N=1-163 P DNA topological change
N=1-163 P endothelial cell chemotaxis
N=1-163 P endothelial cell proliferation
N=1-163 P eye development
N=1-163 P inflammatory response
N=1-163 P inflammatory response to antigenic stimulus
N=1-163 P innate immune response
N=1-163 P lung development
N=1-163 P macrophage activation involved in immune response
N=1-163 P myeloid dendritic cell activation
N=1-163 P negative regulation of apoptotic cell clearance
N=1-163 P negative regulation of blood vessel endothelial cell migration
N=1-163 P negative regulation of CD4-positive, alpha-beta T cell differentiation
N=1-163 P negative regulation of interferon-gamma production
N=1-163 P negative regulation of RNA polymerase II transcription preinitiation complex assembly
N=1-163 P negative regulation of transcription by RNA polymerase II
N=1-163 P neuron projection development
N=1-163 P neutrophil clearance
N=1-163 P neutrophil degranulation
N=1-163 P plasmacytoid dendritic cell activation
N=1-163 P positive regulation of activated T cell proliferation
N=1-163 P positive regulation of apoptotic process
N=1-163 P positive regulation of autophagy
N=1-163 P positive regulation of blood vessel endothelial cell migration
N=1-163 P positive regulation of chemokine (C-X-C motif) ligand 2 production
N=1-163 P positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
N=1-163 P positive regulation of cytosolic calcium ion concentration
N=1-163 P positive regulation of dendritic cell differentiation
N=1-163 P positive regulation of DNA binding
N=1-163 P positive regulation of DNA ligation
N=1-163 P positive regulation of ERK1 and ERK2 cascade
N=1-163 P positive regulation of glycogen catabolic process
N=1-163 P positive regulation of innate immune response
N=1-163 P positive regulation of interferon-alpha production
N=1-163 P positive regulation of interferon-beta production
N=1-163 P positive regulation of interleukin-1 beta production
N=1-163 P positive regulation of interleukin-1 production
N=1-163 P positive regulation of interleukin-10 production
N=1-163 P positive regulation of interleukin-12 production
N=1-163 P positive regulation of interleukin-6 production
N=1-163 P positive regulation of interleukin-8 production
N=1-163 P positive regulation of JNK cascade
N=1-163 P positive regulation of MAPK cascade
N=1-163 P positive regulation of mismatch repair
N=1-163 P positive regulation of monocyte chemotactic protein-1 production
N=1-163 P positive regulation of monocyte chemotaxis
N=1-163 P positive regulation of myeloid cell differentiation
N=1-163 P positive regulation of NIK/NF-kappaB signaling
N=1-163 P positive regulation of sprouting angiogenesis
N=1-163 P positive regulation of toll-like receptor 2 signaling pathway
N=1-163 P positive regulation of toll-like receptor 4 signaling pathway
N=1-163 P positive regulation of toll-like receptor 9 signaling pathway
N=1-163 P positive regulation of transcription by RNA polymerase II
N=1-163 P positive regulation of tumor necrosis factor production
N=1-163 P positive regulation of vascular endothelial cell proliferation
N=1-163 P positive regulation of wound healing
N=1-163 P regulation of nucleotide-excision repair
N=1-163 P regulation of restriction endodeoxyribonuclease activity
N=1-163 P regulation of signaling receptor activity
N=1-163 P regulation of T cell mediated immune response to tumor cell
N=1-163 P regulation of tolerance induction
N=1-163 P regulation of transcription by RNA polymerase II
N=1-163 P regulation of transcription, DNA-templated
N=1-163 P response to glucocorticoid
N=1-163 P T-helper 1 cell activation
N=1-163 P T-helper 1 cell differentiation
N=1-163 P toll-like receptor signaling pathway
N=1-163 P tumor necrosis factor secretion
N=1-163 P V(D)J recombination
N=1-163 P viral process
Sequences
Download file with secondary structure created by Stride  
6cim.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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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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