[English] 日本語
Yorodumi
- PDB-5yhw: Crystal structure of Pig SAMHD1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yhw
TitleCrystal structure of Pig SAMHD1
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / Pig-SAMHD1
Function / homology
Function and homology information


Nucleotide catabolism / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes ...Nucleotide catabolism / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / site of double-strand break / single-stranded DNA binding / defense response to virus / protein homotetramerization / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / 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
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsQin, X.H. / Kong, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400465 China
CitationJournal: Febs J. / Year: 2019
Title: Structural characterization and directed modification of Sus scrofa SAMHD1 reveal the mechanism underlying deoxynucleotide regulation.
Authors: Kong, J. / Wang, M.M. / He, S.Y. / Peng, X. / Qin, X.H.
History
DepositionSep 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _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

-
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
E: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
F: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
G: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
H: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,74748
Polymers486,1868
Non-polymers12,56140
Water77543
1
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
H: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,37424
Polymers243,0934
Non-polymers6,28120
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26790 Å2
ΔGint-93 kcal/mol
Surface area54390 Å2
MethodPISA
2
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
E: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
F: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
G: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,37424
Polymers243,0934
Non-polymers6,28120
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26900 Å2
ΔGint-93 kcal/mol
Surface area54530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.540, 95.909, 130.749
Angle α, β, γ (deg.)78.66, 88.12, 82.68
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1


Mass: 60773.254 Da / Num. of mol.: 8 / Mutation: H206R,D207N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SAMHD1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: I3LG77
#2: Chemical...
ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium acetate trihydrate pH 7.0, 20% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 12, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 108746 / % possible obs: 96.9 % / Redundancy: 3.5 % / Net I/σ(I): 11.8
Reflection shellResolution: 2.7→2.7871 Å / Redundancy: 3.2 % / % possible all: 96.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHENIX(1.10.1_2155)data reduction
PHENIX(1.10.1_2155)data scaling
PHENIX(1.10.1_2155)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZC

4bzc


Resolution: 2.7→29.944 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 46.43
RfactorNum. reflection% reflection
Rfree0.2904 1493 1.37 %
Rwork0.2631 --
obs0.2635 108746 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26154 0 760 43 26957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427572
X-RAY DIFFRACTIONf_angle_d0.65937551
X-RAY DIFFRACTIONf_dihedral_angle_d12.15515945
X-RAY DIFFRACTIONf_chiral_restr0.0464059
X-RAY DIFFRACTIONf_plane_restr0.0044726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78710.38622000.359662X-RAY DIFFRACTION96
2.7871-2.88660.32561000.34759643X-RAY DIFFRACTION96
2.8866-3.00210.3513990.33399863X-RAY DIFFRACTION97
3.0021-3.13860.41242000.31919711X-RAY DIFFRACTION97
3.1386-3.30390.28891000.29679899X-RAY DIFFRACTION98
3.3039-3.51060.32611000.28019902X-RAY DIFFRACTION98
3.5106-3.78110.31161990.25759832X-RAY DIFFRACTION98
3.7811-4.16080.2351000.23489970X-RAY DIFFRACTION99
4.1608-4.76070.2505980.21989901X-RAY DIFFRACTION98
4.7607-5.99020.24581970.23489830X-RAY DIFFRACTION98
5.9902-29.9440.25551000.23439040X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: -8.0476 Å / Origin y: 13.1106 Å / Origin z: 81.0853 Å
111213212223313233
T0.2804 Å2-0.0319 Å20.1213 Å2-0.3618 Å2-0.1265 Å2--0.526 Å2
L0.4185 °2-0.0038 °20.141 °2-0.3614 °2-0.15 °2--0.5951 °2
S0.058 Å °-0.028 Å °0.0965 Å °0.0494 Å °-0.0078 Å °0.056 Å °-0.0907 Å °0.0464 Å °-0.0406 Å °
Refinement TLS groupSelection details: all

+
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