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- PDB-5w1c: Crystal structure of MBP fused activation-induced cytidine deamin... -

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Basic information

Entry
Database: PDB / ID: 5w1c
TitleCrystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with cytidine
Components
  • DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3')
  • DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3')
  • MBP fused activation-induced cytidine deaminase
KeywordsDNA BINDING PROTEIN/DNA / Class switch recombination / Cytidine deaminase / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


somatic diversification of immunoglobulins / regulation of nuclear cell cycle DNA replication / single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / DNA cytosine deamination / cytidine to uridine editing / cytidine deaminase activity / positive regulation of gene expression via chromosomal CpG island demethylation / isotype switching ...somatic diversification of immunoglobulins / regulation of nuclear cell cycle DNA replication / single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / DNA cytosine deamination / cytidine to uridine editing / cytidine deaminase activity / positive regulation of gene expression via chromosomal CpG island demethylation / isotype switching / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / somatic hypermutation of immunoglobulin genes / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / B cell differentiation / Chromatin modifications during the maternal to zygotic transition (MZT) / P-body / mRNA processing / outer membrane-bounded periplasmic space / cellular response to lipopolysaccharide / defense response to virus / defense response to bacterium / ubiquitin protein ligase binding / protein-containing complex / RNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
APOBEC2 / APOBEC-like, N-terminal / APOBEC-like N-terminal domain / : / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. ...APOBEC2 / APOBEC-like, N-terminal / APOBEC-like N-terminal domain / : / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / DNA / DNA (> 10) / Maltose/maltodextrin-binding periplasmic protein / Single-stranded DNA cytosine deaminase
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsQiao, Q. / Wang, L. / Wu, H.
CitationJournal: Mol. Cell / Year: 2017
Title: AID Recognizes Structured DNA for Class Switch Recombination.
Authors: Qiao, Q. / Wang, L. / Meng, F.L. / Hwang, J.K. / Alt, F.W. / Wu, H.
History
DepositionJun 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: MBP fused activation-induced cytidine deaminase
D: DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3')
G: DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3')
A: MBP fused activation-induced cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,18610
Polymers131,4884
Non-polymers6976
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-109 kcal/mol
Surface area51920 Å2
Unit cell
Length a, b, c (Å)125.456, 39.824, 155.304
Angle α, β, γ (deg.)90.00, 90.27, 90.00
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein MBP fused activation-induced cytidine deaminase / MBP / MMBP / Maltodextrin-binding protein / Activation-induced cytidine deaminase / AID / Cytidine ...MBP / MMBP / Maltodextrin-binding protein / Activation-induced cytidine deaminase / AID / Cytidine aminohydrolase


Mass: 62081.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, AICDA, AID / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P0AEY0, UniProt: Q9GZX7, single-stranded DNA cytosine deaminase

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DNA chain , 2 types, 2 molecules DG

#2: DNA chain DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3')


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3')


Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 8 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O5
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M MES at pH 6.2, 3% PEG3350, 10 mM CaCl2 and 20mM Cytidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.18→155.3 Å / Num. obs: 28767 / % possible obs: 99.3 % / Redundancy: 6.5 % / Net I/σ(I): 8.9
Reflection shellResolution: 3.18→3.36 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4138 / CC1/2: 0.974 / Rpim(I) all: 0.335 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W0R

5w0r


Resolution: 3.18→125.455 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2699 1423 5.39 %
Rwork0.232 --
obs0.2341 26403 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.18→125.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8605 484 38 2 9129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089411
X-RAY DIFFRACTIONf_angle_d1.05412874
X-RAY DIFFRACTIONf_dihedral_angle_d23.4983440
X-RAY DIFFRACTIONf_chiral_restr0.0671375
X-RAY DIFFRACTIONf_plane_restr0.0111578
LS refinement shellResolution: 3.1801→3.2937 Å
RfactorNum. reflection
Rfree0.4018 144
Rwork0.3746 -
obs-2491

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