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- PDB-5jj4: Crystal Structure of a Variant Human Activation-induced Deoxycyti... -

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Basic information

Entry
Database: PDB / ID: 5jj4
TitleCrystal Structure of a Variant Human Activation-induced Deoxycytidine Deaminase as an MBP fusion protein
ComponentsMaltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
KeywordsHYDROLASE / AID MBP-fuison Deaminase
Function / homology
Function and homology information


somatic diversification of immunoglobulins / cytidine deamination / regulation of nuclear cell cycle DNA replication / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of gene expression via chromosomal CpG island demethylation / isotype switching ...somatic diversification of immunoglobulins / cytidine deamination / regulation of nuclear cell cycle DNA replication / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of gene expression via chromosomal CpG island demethylation / isotype switching / carbohydrate transmembrane transporter activity / somatic hypermutation of immunoglobulin genes / 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 / cytosol / cytoplasm
Similarity search - Function
APOBEC-like, N-terminal / APOBEC-like N-terminal domain / : / 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 ...APOBEC-like, N-terminal / APOBEC-like N-terminal domain / : / 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
Similarity search - Domain/homology
alpha-maltotetraose / 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: 2.807 Å
AuthorsPedersen, L.C. / Goodman, M.F. / Pham, P. / Afif, S.A.
CitationJournal: DNA Repair (Amst.) / Year: 2016
Title: Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification.
Authors: Pham, P. / Afif, S.A. / Shimoda, M. / Maeda, K. / Sakaguchi, N. / Pedersen, L.C. / Goodman, M.F.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
A: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
B: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,70712
Polymers184,3913
Non-polymers2,3169
Water64936
1
C: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2364
Polymers61,4641
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2364
Polymers61,4641
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2364
Polymers61,4641
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.793, 96.806, 108.692
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase / MBP / MMBP / Maltodextrin-binding protein / Activation-induced cytidine deaminase / Cytidine aminohydrolase


Mass: 61463.652 Da / Num. of mol.: 3 / Fragment: unp residues 27-384, unp residues 3-183
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 / Plasmid: pMALX / Details (production host): fixed arm MBP fusion vector / Production host: Escherichia coli (E. coli) / Strain (production host): CSH50
References: UniProt: P0AEY0, UniProt: Q9GZX7, single-stranded DNA cytosine deaminase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSolubility mutations for MBP: E359A, K362A, D363A Linker residues between MBP and AID: A368, A369, ...Solubility mutations for MBP: E359A, K362A, D363A Linker residues between MBP and AID: A368, A369, A370 Solubility mutations for AID: 1007 N7D, 1008 R8P, 1009 R9H, 1010 K10I, 1012 L12T, 1013 Y13S, 1014 Q14N, 1016 K16N, 1018 V18G, 1019 R19I, Residues 20-22 deleted, 1025 R25H, 1026 E26K, 1032 V32E, 1034 K34E, 1036 R36L

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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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100mM MES pH 6.5, 200mM Calcium Acetate, 15%PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 52735 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DM0 and 3EIU

3dm0

3eiu


Resolution: 2.807→35.475 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1987 3.77 %random selection
Rwork0.1831 ---
obs0.1849 52657 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.807→35.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12546 0 141 36 12723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813058
X-RAY DIFFRACTIONf_angle_d0.81717822
X-RAY DIFFRACTIONf_dihedral_angle_d12.6884483
X-RAY DIFFRACTIONf_chiral_restr0.0461911
X-RAY DIFFRACTIONf_plane_restr0.0032292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8066-2.87680.36491320.30273408X-RAY DIFFRACTION95
2.8768-2.95450.45811410.30093639X-RAY DIFFRACTION100
2.9545-3.04140.37351450.28363624X-RAY DIFFRACTION100
3.0414-3.13950.35941440.26723614X-RAY DIFFRACTION100
3.1395-3.25160.29311410.24513587X-RAY DIFFRACTION100
3.2516-3.38170.24491410.22693638X-RAY DIFFRACTION100
3.3817-3.53550.24691400.19483631X-RAY DIFFRACTION100
3.5355-3.72170.25091480.1853630X-RAY DIFFRACTION100
3.7217-3.95460.23491430.17033624X-RAY DIFFRACTION100
3.9546-4.25950.20611390.1533631X-RAY DIFFRACTION100
4.2595-4.68730.16431470.14063629X-RAY DIFFRACTION100
4.6873-5.36350.18951450.14323659X-RAY DIFFRACTION100
5.3635-6.74990.20821400.18253653X-RAY DIFFRACTION100
6.7499-35.47810.21511410.17023703X-RAY DIFFRACTION99
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)
15.50981.8856-0.51693.16970.92823.3628-0.01380.07390.0814-0.17250.0014-0.499-0.08560.20620.02180.4219-0.0306-0.03220.42540.10660.875358.1518-22.3684233.0727
22.99521.57680.03195.0580.770.24450.3324-0.50470.9530.6132-0.33820.0515-0.21790.09030.00970.6257-0.134-0.06410.6229-0.19830.996546.1892-1.117248.176
33.92380.7691-0.70692.68270.5690.82150.1841-0.44490.95740.0794-0.0539-0.313-0.3090.0884-0.13590.6107-0.1033-0.09220.6664-0.08330.983455.254-6.0997241.384
41.9910.1195-1.05663.69460.6361.80530.0942-0.3160.55220.1919-0.27220.3091-0.25880.00550.19210.5917-0.0975-0.07690.5359-0.140.810944.9986-9.5533244.3518
57.85730.0154-2.12968.3753-0.10435.1293-0.05640.5190.2767-0.5772-0.33170.962-0.4454-0.630.36970.3666-0.0065-0.06330.4012-0.0820.549321.3541-28.7045234.5234
67.99111.23340.06646.56630.26824.99420.09360.0519-0.1010.1912-0.1548-0.13580.02710.0150.04910.338-0.0242-0.00440.25860.0070.443531.4804-39.5973235.7722
71.4311-0.2898-0.35885.12772.31942.60780.1363-0.1676-0.21110.5587-0.70250.67930.3139-0.64340.56930.4411-0.10750.03890.6866-0.14380.617417.6016-38.5999239.9162
82.99190.97251.14152.98510.7093.92550.0055-0.26690.11490.0316-0.01690.1348-0.0848-0.8140.00680.45570.09760.07630.9020.25960.448722.428-7.8584179.2433
92.4751.99420.99092.52492.44822.90680.25340.2704-0.93270.25480.4137-0.76290.77460.2999-0.65920.77370.1511-0.13530.7272-0.00620.905735.8757-31.6976166.4696
102.84210.29580.49593.00490.96892.62840.16940.1498-0.4107-0.06260.08750.12970.4275-0.5896-0.20010.5618-0.0002-0.02360.81480.24370.540721.7825-20.3992168.8052
112.7474-0.3099-3.66471.03270.89787.15670.41760.1157-0.58540.52270.16960.29830.29970.35-0.57040.8704-0.2779-0.07361.50540.23671.090413.6653-28.2474174.7245
121.4059-0.11991.30684.12512.35794.83390.24740.4998-0.212-0.0760.5192-0.64150.18460.7717-0.69760.53950.1275-0.08180.7594-0.06580.889442.716-21.635173.2574
135.8883-0.23160.53263.12770.68183.33150.0497-0.4868-0.05760.03870.0795-0.4266-0.0066-0.2539-0.13420.43940.0796-0.02920.4780.18040.67452.6271-3.0311194.6267
143.0854-0.60520.73083.20771.69894.6091-0.1378-0.2806-0.27210.31580.2017-0.44940.43770.3969-0.11770.56520.1365-0.10870.5990.19031.010565.0865-11.0454193.9393
158.7321-0.11-0.95633.90670.20545.56290.1281-0.1526-0.9710.01850.1520.22930.4798-0.6046-0.30450.4466-0.0045-0.08350.39640.11030.6616-15.9283-11.3526215.1402
164.0413-0.5144-0.64082.27050.25073.67840.1575-0.04950.71-0.04880.094-0.0428-0.4669-0.2087-0.19480.3820.08280.03390.32930.08790.5399-10.86733.6181216.6678
172.2628-0.63741.08611.0668-0.80982.3427-0.0523-0.44810.17020.24970.17370.1267-0.2333-0.4631-0.120.45230.07210.03670.5064-0.05020.4429-7.0618-3.1663236.3067
186.9634-0.3108-0.25325.4877-5.02944.66010.13750.66690.43320.0593-0.1323-0.69330.27991.13150.03860.49280.0152-0.11880.5508-0.06430.478613.623-5.2757233.1372
197.2388-0.119-0.14261.5335-0.79845.43040.2048-0.1823-0.00350.007-0.1621-0.20640.09240.1857-0.03740.4077-0.0113-0.02240.27040.05440.50915.75186.0211207.9555
207.0455-5.9628-7.67985.22096.46718.3981.53381.91390.8027-1.2554-1.1054-0.1556-1.3753-1.1674-0.3750.65890.13930.01680.76050.20250.74349.950412.6821196.5119
214.4229-0.2948-0.85152.8023-0.61764.60440.19040.15850.9088-0.0713-0.0114-0.3519-0.20650.5171-0.14090.4184-0.0644-0.02390.58210.09950.788827.40511.4123205.1877
225.0136-1.28484.21586.594-4.71687.4328-0.07880.3943-1.26080.0421-0.9245-0.05520.27360.30580.73890.34190.10990.01650.5236-0.17130.733446.5329-11.0021235.1723
231.9297-0.77261.89024.9831-1.0645.1540.11990.281-0.061-0.25090.1620.5124-0.0118-0.50480.09350.332-0.0394-0.29910.5980.06680.2889-1.1378-7.2667226.5935
241.0805-2.0361-0.34025.0046-1.47839.70720.2879-0.23230.28420.19680.5803-0.3760.04770.105-0.77530.57520.2120.14620.5706-0.01190.683234.0899-15.3007169.9198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:110 )A1 - 110
2X-RAY DIFFRACTION2( CHAIN A AND RESID 111:183 )A111 - 183
3X-RAY DIFFRACTION3( CHAIN A AND RESID 184:308 )A184 - 308
4X-RAY DIFFRACTION4( CHAIN A AND RESID 309:366 )A309 - 366
5X-RAY DIFFRACTION5( CHAIN A AND RESID 367:1034 )A367 - 1034
6X-RAY DIFFRACTION6( CHAIN A AND RESID 1035:1118 )A1035 - 1118
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1119:1181 )A1119 - 1181
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1:110 )B1 - 110
9X-RAY DIFFRACTION9( CHAIN B AND RESID 111:203 )B111 - 203
10X-RAY DIFFRACTION10( CHAIN B AND RESID 204:304 )B204 - 304
11X-RAY DIFFRACTION11( CHAIN B AND RESID 305:322 )B305 - 322
12X-RAY DIFFRACTION12( CHAIN B AND RESID 323:370 )B323 - 370
13X-RAY DIFFRACTION13( CHAIN B AND RESID 1005:1134 )B1005 - 1134
14X-RAY DIFFRACTION14( CHAIN B AND RESID 1135:1182 )B1135 - 1182
15X-RAY DIFFRACTION15( CHAIN C AND RESID 1:49 )C1 - 49
16X-RAY DIFFRACTION16( CHAIN C AND RESID 50:111 )C50 - 111
17X-RAY DIFFRACTION17( CHAIN C AND RESID 112:342 )C112 - 342
18X-RAY DIFFRACTION18( CHAIN C AND RESID 343:370 )C343 - 370
19X-RAY DIFFRACTION19( CHAIN C AND RESID 1005:1088 )C1005 - 1088
20X-RAY DIFFRACTION20( CHAIN C AND RESID 1089:1105 )C1089 - 1105
21X-RAY DIFFRACTION21( CHAIN C AND RESID 1106:1181 )C1106 - 1181
22X-RAY DIFFRACTION22( CHAIN A AND RESID 1203:1203 )A1203
23X-RAY DIFFRACTION23( CHAIN C AND RESID 1203:1203 )C1203
24X-RAY DIFFRACTION24( CHAIN B AND RESID 1203:1203 )B1203

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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