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- PDB-4cdg: Crystal structure of the Bloom's syndrome helicase BLM in complex... -

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Basic information

Entry
Database: PDB / ID: 4cdg
TitleCrystal structure of the Bloom's syndrome helicase BLM in complex with Nanobody
Components
  • BLOOM SYNDROME PROTEIN
  • NANOBODYSingle-domain antibody
KeywordsHYDROLASE
Function / homology
Function and homology information


regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA/DNA annealing activity / telomere maintenance via semi-conservative replication / cellular response to camptothecin ...regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA/DNA annealing activity / telomere maintenance via semi-conservative replication / cellular response to camptothecin / G-quadruplex DNA unwinding / telomeric D-loop disassembly / t-circle formation / DNA double-strand break processing / Y-form DNA binding / negative regulation of cell division / DNA 3'-5' helicase / four-way junction helicase activity / G-quadruplex DNA binding / cellular response to hydroxyurea / lateral element / negative regulation of DNA recombination / Processive synthesis on the C-strand of the telomere / bubble DNA binding / Impaired BRCA2 binding to PALB2 / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / 3'-5' DNA helicase activity / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / replication fork processing / nuclear chromosome / DNA unwinding involved in DNA replication / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / response to X-ray / ATP-dependent activity, acting on DNA / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / DNA helicase activity / telomere maintenance / replication fork / helicase activity / molecular function activator activity / cellular response to ionizing radiation / double-strand break repair via homologous recombination / protein homooligomerization / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / PML body / Meiotic recombination / nuclear matrix / p53 binding / single-stranded DNA binding / protein complex oligomerization / chromosome / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / DNA repair / DNA damage response / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / protein homodimerization activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / HRDC domain / RQC domain / RQC / RQC domain ...RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / HRDC domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / HRDC-like superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / DNA polymerase; domain 1 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RecQ-like DNA helicase BLM
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 Å
AuthorsNewman, J.A. / Savitsky, P. / Allerston, C.K. / Pike, A.C.W. / Pardon, E. / Steyaert, J. / Arrowsmith, C.H. / von Delft, F. / Bountra, C. / Edwards, A. / Gileadi, O.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Crystal Structure of the Bloom'S Syndrome Helicase Indicates a Role for the Hrdc Domain in Conformational Changes.
Authors: Newman, J.A. / Savitsky, P. / Allerston, C.K. / Bizard, A.H. / Ozer, O. / Sarlos, K. / Liu, Y. / Pardon, E. / Steyaert, J. / Hickson, I.D. / Gileadi, O.
History
DepositionOct 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Source and taxonomy
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Jun 10, 2015Group: Database references
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BLOOM SYNDROME PROTEIN
B: BLOOM SYNDROME PROTEIN
C: NANOBODY
D: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,7368
Polymers185,7514
Non-polymers9854
Water0
1
A: BLOOM SYNDROME PROTEIN
C: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3684
Polymers92,8762
Non-polymers4932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-6.3 kcal/mol
Surface area42550 Å2
MethodPQS
2
B: BLOOM SYNDROME PROTEIN
D: NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3684
Polymers92,8762
Non-polymers4932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-6.1 kcal/mol
Surface area41240 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.666, 88.425, 95.120
Angle α, β, γ (deg.)69.39, 89.84, 77.07
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A )
211(CHAIN B )

NCS oper: (Code: given
Matrix: (-0.9999, 0.01281, -0.00243), (-0.01105, -0.7343, 0.6788), (0.006908, 0.6788, 0.7343)
Vector: 26.8219, 205.117, -97.6843)

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Components

#1: Protein BLOOM SYNDROME PROTEIN / / BLOOM SYNDROME HELICASE / DNA HELICASE / RECQ-LIKE TYPE 2 / RECQ2 / RECQ PROTEIN-LIKE 3


Mass: 76705.219 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE, RESIDUES 636-1298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54132, DNA helicase
#2: Antibody NANOBODY / Single-domain antibody


Mass: 16170.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama)
Description: ISOLATED FROM PHAGE DISPLAY SCREENING OF CDNA OF IMMUNIZED LAMA
Cell: B-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsFIRST TWO RESIDUES ARE REMAINING FROM PURIFICATION TAG AFTER CLEAVAGE ISOLATED FROM IMMUNIZED LAMA, ...FIRST TWO RESIDUES ARE REMAINING FROM PURIFICATION TAG AFTER CLEAVAGE ISOLATED FROM IMMUNIZED LAMA, FIRST 23 RESIDUES ARE SIGNAL SEQUENCE WHICH IS CLEAVED OFF DURING EXPRESSION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.92 % / Description: NONE
Crystal growDetails: 0.1M MES PH 6.0, 22% PEG 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→88 Å / Num. obs: 43258 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 67.06 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WWY

2wwy


Resolution: 2.794→42.881 Å / SU ML: 0.4 / σ(F): 0.02 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 4345 5 %
Rwork0.2056 --
obs0.2076 43172 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.6 Å2
Refinement stepCycle: LAST / Resolution: 2.794→42.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11655 0 56 0 11711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211946
X-RAY DIFFRACTIONf_angle_d0.65116162
X-RAY DIFFRACTIONf_dihedral_angle_d13.5714362
X-RAY DIFFRACTIONf_chiral_restr0.0261814
X-RAY DIFFRACTIONf_plane_restr0.0032061
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL0.4
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7936-2.82540.36611400.32342364X-RAY DIFFRACTION85
2.8254-2.85860.36411380.30422751X-RAY DIFFRACTION98
2.8586-2.89350.30131340.28862658X-RAY DIFFRACTION98
2.8935-2.93010.32421440.28662735X-RAY DIFFRACTION98
2.9301-2.96860.36231740.27542772X-RAY DIFFRACTION99
2.9686-3.00930.33781240.28092692X-RAY DIFFRACTION98
3.0093-3.05230.29611520.27952736X-RAY DIFFRACTION99
3.0523-3.09780.37281500.28532736X-RAY DIFFRACTION99
3.0978-3.14620.36651420.28552777X-RAY DIFFRACTION99
3.1462-3.19780.33851140.2782679X-RAY DIFFRACTION98
3.1978-3.25290.34171500.27712790X-RAY DIFFRACTION99
3.2529-3.3120.34081180.26822807X-RAY DIFFRACTION99
3.312-3.37570.29171500.25432722X-RAY DIFFRACTION99
3.3757-3.44460.32871280.24682710X-RAY DIFFRACTION99
3.4446-3.51940.30961620.23542840X-RAY DIFFRACTION99
3.5194-3.60130.26271680.23722626X-RAY DIFFRACTION99
3.6013-3.69130.26591340.232802X-RAY DIFFRACTION99
3.6913-3.7910.33211440.23692718X-RAY DIFFRACTION99
3.791-3.90250.27741220.20462762X-RAY DIFFRACTION99
3.9025-4.02840.22971520.20062752X-RAY DIFFRACTION99
4.0284-4.17220.23831500.18372740X-RAY DIFFRACTION99
4.1722-4.33910.21261420.16522796X-RAY DIFFRACTION99
4.3391-4.53640.18671500.15662728X-RAY DIFFRACTION99
4.5364-4.77530.15671560.15822704X-RAY DIFFRACTION99
4.7753-5.0740.20421510.16822786X-RAY DIFFRACTION99
5.074-5.46510.21461600.18192740X-RAY DIFFRACTION100
5.4651-6.01370.17221480.18922758X-RAY DIFFRACTION100
6.0137-6.88080.2441500.19182762X-RAY DIFFRACTION100
6.8808-8.65740.17821640.17362772X-RAY DIFFRACTION100
8.6574-42.88620.22421340.16682738X-RAY DIFFRACTION99

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