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- PDB-3gna: Crystal structure of the RAG1 nonamer-binding domain with DNA -

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Basic information

Entry
Database: PDB / ID: 3gna
TitleCrystal structure of the RAG1 nonamer-binding domain with DNA
Components
  • 5'-D(*AP*CP*TP*TP*AP*AP*CP*AP*AP*AP*AP*AP*CP*C)-3'
  • 5'-D(*TP*GP*GP*TP*TP*TP*TP*TP*GP*TP*TP*AP*AP*G)-3'
  • V(D)J recombination-activating protein 1
KeywordsRECOMBINATION / vdj recombination / DNA recombination / DNA-binding / Endonuclease / Hydrolase / Metal-binding / Nuclease / Nucleus / Zinc-finger / Amino-acid biosynthesis / Isomerase / Lysine biosynthesis
Function / homology
Function and homology information


DNA recombinase complex / endodeoxyribonuclease complex / pre-B cell allelic exclusion / regulation of behavioral fear response / V(D)J recombination / negative regulation of T cell apoptotic process / negative regulation of thymocyte apoptotic process / positive regulation of T cell differentiation / regulation of T cell differentiation / T cell homeostasis ...DNA recombinase complex / endodeoxyribonuclease complex / pre-B cell allelic exclusion / regulation of behavioral fear response / V(D)J recombination / negative regulation of T cell apoptotic process / negative regulation of thymocyte apoptotic process / positive regulation of T cell differentiation / regulation of T cell differentiation / T cell homeostasis / protein autoubiquitination / B cell differentiation / thymus development / visual learning / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell differentiation in thymus / chromatin organization / histone binding / endonuclease activity / DNA recombination / sequence-specific DNA binding / adaptive immune response / Hydrolases; Acting on ester bonds / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus
Similarity search - Function
Helix Hairpins - #510 / Recombination-activating protein 1 zinc-finger domain / V(D)J recombination-activating protein 1, Zinc finger / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding / Recombination-activation protein 1 (RAG1), recombinase ...Helix Hairpins - #510 / Recombination-activating protein 1 zinc-finger domain / V(D)J recombination-activating protein 1, Zinc finger / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding / Recombination-activation protein 1 (RAG1), recombinase / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Helix Hairpins / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger C2H2 superfamily / Ring finger / Helix non-globular / Zinc finger RING-type profile. / Zinc finger, RING-type / Special / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / V(D)J recombination-activating protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsYin, F.F. / Bailey, S. / Innis, C.A. / Steitz, T.A. / Schatz, D.G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis.
Authors: Yin, F.F. / Bailey, S. / Innis, C.A. / Ciubotaru, M. / Kamtekar, S. / Steitz, T.A. / Schatz, D.G.
History
DepositionMar 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V(D)J recombination-activating protein 1
D: 5'-D(*AP*CP*TP*TP*AP*AP*CP*AP*AP*AP*AP*AP*CP*C)-3'
E: 5'-D(*TP*GP*GP*TP*TP*TP*TP*TP*GP*TP*TP*AP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)19,3633
Polymers19,3633
Non-polymers00
Water1448
1
A: V(D)J recombination-activating protein 1
D: 5'-D(*AP*CP*TP*TP*AP*AP*CP*AP*AP*AP*AP*AP*CP*C)-3'
E: 5'-D(*TP*GP*GP*TP*TP*TP*TP*TP*GP*TP*TP*AP*AP*G)-3'

A: V(D)J recombination-activating protein 1
D: 5'-D(*AP*CP*TP*TP*AP*AP*CP*AP*AP*AP*AP*AP*CP*C)-3'
E: 5'-D(*TP*GP*GP*TP*TP*TP*TP*TP*GP*TP*TP*AP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)38,7266
Polymers38,7266
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)97.470, 97.470, 69.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-6-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 3 / Auth seq-ID: 1 - 14 / Label seq-ID: 1 - 14

Dom-IDBeg auth comp-IDBeg label alt-IDBeg label comp-IDEnd auth comp-IDEnd label alt-IDEnd label comp-IDAuth asym-IDLabel asym-ID
1DAADADCADCDB
2DTBDTDGBDGEC

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Components

#1: Protein V(D)J recombination-activating protein 1 / RAG-1


Mass: 10805.378 Da / Num. of mol.: 1 / Fragment: Nonamer binding domain: UNP residues 389-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag1, Rag-1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15919
#2: DNA chain 5'-D(*AP*CP*TP*TP*AP*AP*CP*AP*AP*AP*AP*AP*CP*C)-3'


Mass: 4225.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#3: DNA chain 5'-D(*TP*GP*GP*TP*TP*TP*TP*TP*GP*TP*TP*AP*AP*G)-3'


Mass: 4331.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2PEG 40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2008
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 11093 / Num. obs: 7526 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.048
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 1 / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU B: 27.231 / SU ML: 0.286 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.428 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27063 330 4.8 %RANDOM
Rwork0.23642 ---
obs0.23789 6475 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 80.982 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2--2.06 Å20 Å2
3----4.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms553 549 0 8 1110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211176
X-RAY DIFFRACTIONr_bond_other_d0.0030.02670
X-RAY DIFFRACTIONr_angle_refined_deg1.2042.5471693
X-RAY DIFFRACTIONr_angle_other_deg0.90931647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.063569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.52822.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8415117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.929159
X-RAY DIFFRACTIONr_chiral_restr0.0540.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02891
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02119
X-RAY DIFFRACTIONr_nbd_refined0.1920.2147
X-RAY DIFFRACTIONr_nbd_other0.1770.2536
X-RAY DIFFRACTIONr_nbtor_refined0.2070.2425
X-RAY DIFFRACTIONr_nbtor_other0.0810.2429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0790.215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.23
X-RAY DIFFRACTIONr_mcbond_it0.5521.5356
X-RAY DIFFRACTIONr_mcbond_other0.1361.5139
X-RAY DIFFRACTIONr_mcangle_it0.882538
X-RAY DIFFRACTIONr_scbond_it0.65721103
X-RAY DIFFRACTIONr_scangle_it0.9442.51154
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: D / Ens-ID: 1 / Number: 59 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.11
loose thermal0.5410
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.49 28 -
Rwork0.444 445 -
obs--98.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.06280.4907-0.48023.2553-29.77360.5327-0.8687-0.91190.38310.05450.529-0.0588-1.4473-0.5872-0.1524-0.05410.1755-0.2498-0.0579-0.147648.655713.61510.0047
24.8448-2.5641-1.75955.41011.22827.2146-0.2851-0.4014-0.61150.14320.15560.43410.12350.38540.1295-0.19170.14490.0414-0.1794-0.001-0.187428.130424.0217-0.9018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 14
2X-RAY DIFFRACTION1E1 - 14
3X-RAY DIFFRACTION2A389 - 456

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