[English] 日本語
Yorodumi
- PDB-7kzg: Human MBD4 glycosylase domain bound to DNA containing oxacarbeniu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kzg
TitleHuman MBD4 glycosylase domain bound to DNA containing oxacarbenium-ion analog 1-aza-2'-deoxyribose
Components
  • DNA (5'-D(*CP*CP*AP*GP*CP*GP*(NR1)P*GP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')
  • Methyl-CpG-binding domain protein 4
KeywordsHYDROLASE/DNA / protein-DNA complex / HYDROLASE-DNA complex
Function / homology
Function and homology information


satellite DNA binding / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA endonuclease activity / response to estradiol ...satellite DNA binding / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA endonuclease activity / response to estradiol / nuclear speck / DNA repair / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Methyl-CpG-binding domain protein 4 / Methyl-CpG binding protein MeCP2/MBD4 / DNA glycosylase / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Methyl-CpG-binding domain protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsPidugu, L.S. / Pozharski, E. / Drohat, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM072711, R35-GM136225 United States
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural Insights into the Mechanism of Base Excision by MBD4.
Authors: Pidugu, L.S. / Bright, H. / Lin, W.J. / Majumdar, C. / Van Ostrand, R.P. / David, S.S. / Pozharski, E. / Drohat, A.C.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyl-CpG-binding domain protein 4
C: DNA (5'-D(*CP*CP*AP*GP*CP*GP*(NR1)P*GP*CP*AP*GP*C)-3')
D: DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,37511
Polymers27,7803
Non-polymers5958
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-44 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.465, 56.414, 102.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Methyl-CpG-binding domain protein 4 / / Methyl-CpG-binding endonuclease 1 / Methyl-CpG-binding protein MBD4 / Mismatch-specific DNA N-glycosylase


Mass: 20560.615 Da / Num. of mol.: 1 / Fragment: glycosylase domain (UNP residues 426-580)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Production host: Escherichia coli (E. coli)
References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

-
DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*CP*GP*(NR1)P*GP*CP*AP*GP*C)-3')


Mass: 3524.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3')


Mass: 3695.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 6 types, 243 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG1000, HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.68→37.98 Å / Num. obs: 28121 / % possible obs: 99.6 % / Redundancy: 13.1 % / CC1/2: 0.994 / Rpim(I) all: 0.091 / Rrim(I) all: 0.333 / Net I/σ(I): 10.2 / Num. measured all: 367050 / Scaling rejects: 251
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.68-1.7113.31907714290.4161.7236.4031.5100
9.05-37.9811.526432300.9730.030.09735.399.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DK9

4dk9


Resolution: 1.68→37.98 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 1429 5.1 %
Rwork0.1681 26617 -
obs0.1699 28046 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.18 Å2 / Biso mean: 27.4813 Å2 / Biso min: 9.49 Å2
Refinement stepCycle: final / Resolution: 1.68→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 478 37 242 1968
Biso mean--37.81 38.93 -
Num. residues----168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.740.26621430.26132600274399
1.74-1.810.27281460.235426322778100
1.81-1.890.22291320.21612596272898
1.89-1.990.2261460.191726212767100
1.99-2.120.21791250.173926592784100
2.12-2.280.20071540.17226502804100
2.28-2.510.19061510.16162635278699
2.51-2.870.20581400.158726902830100
2.87-3.620.1971460.15262682282899
3.62-37.980.18711460.15082852299899
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)
12.8541-0.32621.19181.79011.04282.49860.0405-0.30530.49720.0811-0.05880.0725-0.2435-0.1931-0.0090.1740.00920.00140.1887-0.00480.20675.215217.849317.252
22.62521.21010.08785.30480.22652.8507-0.0495-0.1089-0.0707-0.07130.05660.0913-0.0359-0.0554-0.00970.08910.0134-0.00760.12240.00730.085813.59996.322917.8962
31.96252.74721.77744.63810.94495.90290.2776-0.39490.24550.5196-0.19770.29830.0392-0.1175-0.04870.19740.03630.04230.138-0.00310.124812.63856.31527.6359
44.13940.0939-0.12974.23760.3024.00780.048-0.2630.09390.4924-0.0139-0.3454-0.12820.1189-0.04610.1675-0.0081-0.04270.1465-0.03440.138427.05759.617524.2087
52.92583.42210.09774.67071.42446.74580.0116-0.5645-0.18980.34610.0183-0.2502-0.0470.24410.00040.22190.0524-0.02720.17540.02270.139320.5953-2.790425.9434
62.99182.7884-1.42056.6237-2.64643.5648-0.0491-0.0022-0.0596-0.1549-0.0025-0.30470.11080.23860.06490.09460.0173-0.00910.1252-0.00660.112524.12584.081817.0816
76.19210.67811.18354.0923-0.7455.36990.06330.39870.1783-0.0389-0.0502-0.2372-0.09890.29180.01110.1260.01380.00960.13390.0170.096521.916211.24817.3057
84.3894-0.98871.24244.72561.72082.37080.12790.1070.0982-0.1734-0.07160.26040.0861-0.2487-0.05640.1183-0.0038-0.01080.13160.02830.110210.80912.05868.4688
94.41920.90966.21831.72641.70258.9246-0.27110.12450.3632-0.26870.0109-0.2531-0.61490.14640.26420.2115-0.00030.01420.16090.05340.19528.233419.83785.0226
106.64212.7686-2.53014.3344-5.22536.43120.03570.2777-0.2377-0.4710.0062-0.14750.88830.1085-0.0810.24970.0542-0.05860.145-0.01120.11145.18948.26733.5574
114.317-2.52262.0214.394-2.37536.53120.1364-0.0789-0.1001-0.22370.09190.37610.193-0.4175-0.23990.1458-0.0165-0.01780.17380.01410.1767-1.539513.17628.2296
120.9869-0.63340.46980.90251.63227.77130.17760.1420.7818-1.2478-0.2863-0.4741-1.0180.7334-0.07450.42080.04190.06280.47640.14050.4796-2.832425.42586.9829
130.86710.9272-0.10553.0846-1.37073.0575-0.29060.2325-0.4928-0.44370.20560.05010.588-0.27620.15190.2158-0.03440.01770.163-0.00990.28259.1692-8.270313.8219
144.87150.35960.42721.64130.37881.3961-0.17810.0831-0.0641-0.41980.33620.54160.4838-0.2357-0.02080.2816-0.0621-0.03730.18440.10370.32537.973-9.989816.5287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 437 through 455 )A437 - 455
2X-RAY DIFFRACTION2chain 'A' and (resid 456 through 470 )A456 - 470
3X-RAY DIFFRACTION3chain 'A' and (resid 471 through 484 )A471 - 484
4X-RAY DIFFRACTION4chain 'A' and (resid 485 through 495 )A485 - 495
5X-RAY DIFFRACTION5chain 'A' and (resid 496 through 508 )A496 - 508
6X-RAY DIFFRACTION6chain 'A' and (resid 509 through 525 )A509 - 525
7X-RAY DIFFRACTION7chain 'A' and (resid 526 through 538 )A526 - 538
8X-RAY DIFFRACTION8chain 'A' and (resid 539 through 548 )A539 - 548
9X-RAY DIFFRACTION9chain 'A' and (resid 549 through 555 )A549 - 555
10X-RAY DIFFRACTION10chain 'A' and (resid 556 through 560 )A556 - 560
11X-RAY DIFFRACTION11chain 'A' and (resid 561 through 573 )A561 - 573
12X-RAY DIFFRACTION12chain 'A' and (resid 574 through 580 )A574 - 580
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 12 )C1 - 12
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 12 )D1 - 12

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • 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

-
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

Read more