[English] 日本語
Yorodumi
- PDB-4to0: Structure basis of cellular dNTP regulation, SAMHD1-GTP-dATP-dCTP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4to0
TitleStructure basis of cellular dNTP regulation, SAMHD1-GTP-dATP-dCTP complex
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / SAMHD1 / HIV / restriction factor / dNTPase / dNTP regulation / host pathogen interaction
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / regulation of innate immune response / negative regulation of type I interferon-mediated signaling pathway / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain ...Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJi, X. / Tang, C. / Zhao, Q. / Wang, W. / Xiong, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI097064 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis of cellular dNTP regulation by SAMHD1.
Authors: Ji, X. / Tang, C. / Zhao, Q. / Wang, W. / Xiong, Y.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 2.0Mar 30, 2022Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site_anisotrop / citation ...atom_site_anisotrop / citation / database_2 / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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.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 / _struct_keywords.text
Revision 2.1Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,44020
Polymers238,4174
Non-polymers6,02316
Water2,504139
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28810 Å2
ΔGint-57 kcal/mol
Surface area68470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.418, 141.329, 97.519
Angle α, β, γ (deg.)90.000, 114.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTRPTRPAA114 - 5982 - 486
21THRTHRTRPTRPBB114 - 5982 - 486
12THRTHRTRPTRPAA114 - 5982 - 486
22THRTHRTRPTRPCC114 - 5982 - 486
13THRTHRASNASNAA114 - 5992 - 487
23THRTHRASNASNDD114 - 5992 - 487
14ASPASPTRPTRPBB113 - 5981 - 486
24ASPASPTRPTRPCC113 - 5981 - 486
15ASPASPASNASNBB113 - 5991 - 487
25ASPASPASNASNDD113 - 5991 - 487
16ASPASPTRPTRPCC113 - 5981 - 486
26ASPASPTRPTRPDD113 - 5981 - 486

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM ...dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM domain and HD domain-containing protein 1


Mass: 59604.172 Da / Num. of mol.: 4 / Fragment: UNP residues 113-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases

-
Non-polymers , 5 types, 155 molecules

#2: Chemical
ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 298 K / Method: batch mode / Details: SPG buffer, PEG 1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 87303 / % possible obs: 98.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.115 / Χ2: 1.028 / Net I/av σ(I): 8.26 / Net I/σ(I): 8.6 / Num. measured all: 279499
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.3-2.342.843251.02497.6
2.34-2.382.843361.02397.2
2.38-2.433.243620.99599.2
2.43-2.483.243311.03399.10.989
2.48-2.533.243761.03898.80.858
2.53-2.593.243571.028990.749
2.59-2.663.243531.07498.60.634
2.66-2.733.243741.12998.60.496
2.73-2.813.143691.10198.50.408
2.81-2.92.842541.07296.50.345
2.9-33.343751.0399.10.274
3-3.123.444121.04899.40.22
3.12-3.263.443791.00399.10.181
3.26-3.443.343690.96698.70.143
3.44-3.653.243430.96898.20.118
3.65-3.933.143210.98897.80.099
3.93-4.333.544301.0199.40.087
4.33-4.953.443901.01398.80.078
4.95-6.243.243741.008980.081
6.24-503.444731.01798.50.076

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZB

4bzb


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 21.054 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 4490 5.1 %RANDOM
Rwork0.191 82770 --
obs0.1926 87260 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 167.13 Å2 / Biso mean: 45.231 Å2 / Biso min: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å2-2.43 Å2
2--0.03 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15723 0 364 139 16226
Biso mean--35.48 48.55 -
Num. residues----1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01916495
X-RAY DIFFRACTIONr_bond_other_d0.0070.0215642
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.98422355
X-RAY DIFFRACTIONr_angle_other_deg1.294336020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.22851922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63723.968809
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.752152923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.90415112
X-RAY DIFFRACTIONr_chiral_restr0.090.22356
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118279
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023885
X-RAY DIFFRACTIONr_mcbond_it3.3924.0847703
X-RAY DIFFRACTIONr_mcbond_other3.3924.0837702
X-RAY DIFFRACTIONr_mcangle_it5.1656.1199620
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A305160.09
12B305160.09
21A303950.09
22C303950.09
31A306580.09
32D306580.09
41B304950.09
42C304950.09
51B306690.08
52D306690.08
61C307220.09
62D307220.09
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 297 -
Rwork0.343 5596 -
all-5893 -
obs--89.6 %
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)
10.64360.0090.28510.29540.0680.4498-0.031-0.1524-0.09360.1560.0319-0.01580.07710.0823-0.00090.13630.03520.03040.1120.03040.036340.759-4.180434.8513
20.39520.00070.20190.4139-0.0590.35340.02210.0365-0.0403-0.0361-0.04930.1423-0.0218-0.01430.02720.0570.01060.02870.0162-0.03450.134311.05582.3247-5.1893
30.64730.01540.330.5580.28770.6144-0.00860.1297-0.0137-0.05870.0004-0.0919-0.09080.19680.00820.0851-0.05650.05680.0967-0.00190.077244.24514.77121.0745
40.6386-0.06310.25530.39890.08780.5975-0.004-0.2543-0.01880.1345-0.04680.1352-0.0349-0.20880.05080.1126-0.0180.10320.132-0.02990.11256.53897.05433.3742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A114 - 599
2X-RAY DIFFRACTION2B113 - 599
3X-RAY DIFFRACTION3C113 - 598
4X-RAY DIFFRACTION4D113 - 599

+
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