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- PDB-5w0r: Crystal structure of MBP fused activation-induced cytidine deamin... -

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Basic information

Entry
Database: PDB / ID: 5w0r
TitleCrystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with cacodylic acid
ComponentsMBP fused activation-induced cytidine deaminase
KeywordsHYDROLASE / Class switch recombination / Cytidine deaminase
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
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 ...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
CACODYLATE ION / 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: 2.4 Å
AuthorsQiao, Q. / Wang, L. / Wu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
Cancer Research Institute United States
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
DepositionMay 31, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

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Assembly

Deposited unit
B: MBP fused activation-induced cytidine deaminase
A: MBP fused activation-induced cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8058
Polymers123,3202
Non-polymers4856
Water3,225179
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B: MBP fused activation-induced cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9024
Polymers61,6601
Non-polymers2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: MBP fused activation-induced cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9024
Polymers61,6601
Non-polymers2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.960, 179.070, 188.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MBP fused activation-induced cytidine deaminase


Mass: 61659.883 Da / Num. of mol.: 2
Fragment: UNP P0AEY0 residues 27-392, UNP Q9GZX7 residues 13-181
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.05 M sodium cacodylate at pH 5.5, 20 mM MgCl2, 10 mM CaCl2, 10 mM spermidine, 5% PEG3350

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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: 2.4→188.1 Å / Num. obs: 48976 / % possible obs: 99.3 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.4
Reflection shellResolution: 2.42→2.5 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.354 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 53182 / CC1/2: 0.883 / Rpim(I) all: 0.577 / % possible all: 84.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VD8, 3VOW

3vd8

3vow


Resolution: 2.4→24.809 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 2492 5.09 %RANDOM
Rwork0.2193 ---
obs0.2203 48976 97.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→24.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8642 0 14 179 8835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058929
X-RAY DIFFRACTIONf_angle_d0.93512117
X-RAY DIFFRACTIONf_dihedral_angle_d14.6933257
X-RAY DIFFRACTIONf_chiral_restr0.0361284
X-RAY DIFFRACTIONf_plane_restr0.0041567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44610.3702970.32351810X-RAY DIFFRACTION68
2.4461-2.4960.32421320.31272419X-RAY DIFFRACTION93
2.496-2.55020.33751250.3132571X-RAY DIFFRACTION100
2.5502-2.60950.30711640.29982598X-RAY DIFFRACTION100
2.6095-2.67470.29631590.28722593X-RAY DIFFRACTION100
2.6747-2.74690.30171130.27142583X-RAY DIFFRACTION99
2.7469-2.82760.30331420.26222648X-RAY DIFFRACTION100
2.8276-2.91880.30531400.24712568X-RAY DIFFRACTION100
2.9188-3.02290.29361460.252642X-RAY DIFFRACTION100
3.0229-3.14370.34831590.24962603X-RAY DIFFRACTION100
3.1437-3.28650.27091350.24432624X-RAY DIFFRACTION100
3.2865-3.45930.2311250.22432608X-RAY DIFFRACTION98
3.4593-3.67540.23751310.20622699X-RAY DIFFRACTION100
3.6754-3.95810.1971240.19182633X-RAY DIFFRACTION100
3.9581-4.35450.17851410.17852669X-RAY DIFFRACTION99
4.3545-4.98020.18641480.16142657X-RAY DIFFRACTION99
4.9802-6.25780.19851580.20842740X-RAY DIFFRACTION100
6.2578-24.81010.19941530.18862819X-RAY DIFFRACTION98
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)
10.66190.2396-0.59010.2506-0.18524.3486-0.03450.01480.01090.09880.01980.00670.3047-0.4589-0.00260.2163-0.0377-0.02090.316-0.06580.32155.1354-45.33127.8852
22.5766-1.30740.52031.91810.37343.4383-0.09050.2210.0395-0.01540.07170.1079-0.5644-0.21710.00960.2441-0.02240.02720.21320.05040.3097-1.5285-8.564720.3483
31.5565-0.56781.27130.98960.32584.13190.1772-0.1123-0.01060.0679-0.05390.0791-0.1202-0.5792-0.14560.3231-0.04450.07910.26430.01630.2617-0.4543-12.526960.2178
42.60421.11670.84282.34770.42834.0208-0.0183-0.07560.01310.17450.0845-0.3331-0.3686-0.3101-0.16760.30010.0447-0.02260.315-0.06110.31310.0992-13.019684.6828
50.9263-0.31761.50250.7336-0.13664.1987-0.0129-0.0073-0.01860.02420.2405-0.1739-0.5246-0.0095-0.14890.3121-0.01590.06940.2393-0.05320.29297.0258-13.433168.6469
63.61280.184-1.06451.9907-0.21615.2407-0.28080.0915-0.15370.05230.1870.01890.4295-0.72720.06770.2484-0.08050.03840.3026-0.0220.2627-5.5523-49.404176.3172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 3:353 )B3 - 353
2X-RAY DIFFRACTION2( CHAIN B AND RESID 354:373 )B354 - 373
3X-RAY DIFFRACTION3( CHAIN A AND RESID 2:132 )A2 - 132
4X-RAY DIFFRACTION4( CHAIN A AND RESID 133:242 )A133 - 242
5X-RAY DIFFRACTION5( CHAIN A AND RESID 243:369 )A243 - 369
6X-RAY DIFFRACTION6( CHAIN A AND RESID 370:373 )A370 - 373

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