[English] 日本語
Yorodumi
- PDB-4zwe: Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zwe
TitleCrystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / Phosphorylation / Tetramer stability / dNTPase / HIV-1 Restriction
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / dGTP catabolic process / 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 / Interferon alpha/beta signaling / site of double-strand break / single-stranded DNA binding / 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. / Sterile alpha motif. / Metal dependent phosphohydrolases with conserved 'HD' 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. / Sterile alpha motif. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsTang, C. / Ji, X. / Xiong, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI102778 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Impaired dNTPase Activity of SAMHD1 by Phosphomimetic Mutation of Thr-592.
Authors: Tang, C. / Ji, X. / Wu, L. / Xiong, Y.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.4Sep 27, 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 / struct_ncs_dom_lim
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_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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)244,61721
Polymers238,4094
Non-polymers6,20817
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28290 Å2
ΔGint-55 kcal/mol
Surface area68700 Å2
MethodPISA
2
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,80311
Polymers119,2042
Non-polymers3,5999
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-24 kcal/mol
Surface area39690 Å2
MethodPISA
3
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,29610
Polymers119,2042
Non-polymers3,0928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-16 kcal/mol
Surface area39950 Å2
MethodPISA
4
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,81310
Polymers119,2042
Non-polymers2,6098
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-34 kcal/mol
Surface area39800 Å2
MethodPISA
5
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,32011
Polymers119,2042
Non-polymers3,1169
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-28 kcal/mol
Surface area39910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.083, 146.091, 98.463
Angle α, β, γ (deg.)90.000, 115.030, 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: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 114 - 599 / Label seq-ID: 2 - 487

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#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: 59602.203 Da / Num. of mol.: 4 / Fragment: residues 113-626 / Mutation: H206R, D207N, T592V
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
#2: Chemical
ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.4 / 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 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 54764 / % possible obs: 98.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.099 / Rrim(I) all: 0.199 / Χ2: 1.001 / Net I/av σ(I): 8.714 / Net I/σ(I): 3.2 / Num. measured all: 379452
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.8-2.857.127440.3330.7360.91199.7
2.85-2.97.127260.3930.6460.92398.8
2.9-2.96727640.4370.590.93499.3
2.96-3.02727220.5570.5120.92199.1
3.02-3.08727250.5750.4660.92698.8
3.08-3.156.927720.6380.3850.95198.80.94
3.15-3.236.726950.6990.3370.94299.10.8130.882
3.23-3.326.326880.7620.2850.95497.40.6690.729
3.32-3.426.826830.8650.2240.9797.30.5460.591
3.42-3.537.227860.9070.1850.96999.30.4650.501
3.53-3.657.127270.9450.1480.9999.30.3690.398
3.65-3.87.127360.9610.1161.03499.50.290.313
3.8-3.97727650.9750.0921.06399.50.2270.245
3.97-4.186.827550.9780.0781.09899.20.190.206
4.18-4.446.426710.9830.0661.124960.1560.169
4.44-4.797.227730.9870.0571.09499.70.1420.153
4.79-5.277.227490.9890.0551.06399.40.1390.149
5.27-6.03727840.9870.0581.0599.30.1420.153
6.03-7.596.827050.9910.0441.04796.90.1070.116
7.59-506.927940.9940.0331.06980.0810.088

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZB

4bzb


Resolution: 2.81→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 39.58 / SU ML: 0.334 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 2789 5.1 %RANDOM
Rwork0.208 ---
obs0.2101 51938 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.06 Å2 / Biso mean: 70.01 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å21.59 Å2
2---1.21 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15700 0 377 3 16080
Biso mean--70.62 54.97 -
Num. residues----1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916484
X-RAY DIFFRACTIONr_bond_other_d0.0070.0215639
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.98622342
X-RAY DIFFRACTIONr_angle_other_deg1.425336005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.90751916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08223.975810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.365152924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.26115112
X-RAY DIFFRACTIONr_chiral_restr0.0730.22346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118258
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023882
X-RAY DIFFRACTIONr_mcbond_it3.1344.9057682
X-RAY DIFFRACTIONr_mcbond_other3.1334.9057681
X-RAY DIFFRACTIONr_mcangle_it4.937.3579592
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A301540.12
12B301540.12
21A304460.11
22C304460.11
31A303780.11
32D303780.11
41B302740.12
42C302740.12
51B301580.12
52D301580.12
61C304070.11
62D304070.11
LS refinement shellResolution: 2.806→2.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 178 -
Rwork0.308 3564 -
all-3742 -
obs--91.07 %
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)
10.48070.0869-0.1480.57890.05510.2616-0.03460.03140.02060.0245-0.00570.1336-0.0471-0.07650.04030.26590.0026-0.17220.0239-0.00010.1528-21.33133.870243.3058
20.62840.1621-0.17450.32730.23410.7329-0.06280.1598-0.0585-0.10170.1229-0.1063-0.11920.1447-0.06010.3064-0.0647-0.12030.1228-0.03640.121817.1531-0.760111.2939
30.46720.1239-0.02340.50020.16120.3692-0.11850.214-0.1049-0.08320.05090.04690.0849-0.0770.06760.3403-0.0727-0.13570.1158-0.05640.1394-15.5163-16.13310.3591
40.4537-0.0186-0.02890.76350.03340.33190.0172-0.0917-0.06140.10110.0413-0.16160.0490.1142-0.05840.28170.0054-0.20880.0556-0.00620.172713.3121-3.981250.1114
51.20821.8181.32132.7482.02121.5746-0.0632-0.00890.3214-0.0575-0.00690.44850.07510.00720.070.3664-0.0558-0.28820.1880.00341.0306-22.15093.296342.8916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A114 - 599
2X-RAY DIFFRACTION1A700 - 900
3X-RAY DIFFRACTION2B114 - 599
4X-RAY DIFFRACTION2B700 - 900
5X-RAY DIFFRACTION3C114 - 599
6X-RAY DIFFRACTION3C700 - 900
7X-RAY DIFFRACTION4D114 - 599
8X-RAY DIFFRACTION4D700 - 900
9X-RAY DIFFRACTION5E1 - 28

+
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://pdbjlvh1.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