[English] 日本語
Yorodumi
- PDB-32jd: Structure of the pathogenic variant P157S of Human SHMT2 in a dis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 32jd
TitleStructure of the pathogenic variant P157S of Human SHMT2 in a distorted tetrameric conformation
ComponentsSerine hydroxymethyltransferase, mitochondrial
KeywordsTRANSFERASE
Function / homology
Function and homology information


formate biosynthetic process / hydroxytrimethyllysine aldolase activity / BRISC complex / glycine metabolic process / L-allo-threonine aldolase activity / response to vitamin B6 / regulation of mitochondrial translation / regulation of oxidative phosphorylation / L-serine metabolic process / L-serine biosynthetic process ...formate biosynthetic process / hydroxytrimethyllysine aldolase activity / BRISC complex / glycine metabolic process / L-allo-threonine aldolase activity / response to vitamin B6 / regulation of mitochondrial translation / regulation of oxidative phosphorylation / L-serine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / : / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to type I interferon / tetrahydrofolate interconversion / protein K63-linked deubiquitination / regulation of aerobic respiration / amino acid binding / RHOG GTPase cycle / mitochondrial nucleoid / one-carbon metabolic process / Mitochondrial protein degradation / protein tetramerization / pyridoxal phosphate binding / protein homotetramerization / mitochondrial inner membrane / mitochondrial matrix / positive regulation of cell population proliferation / chromatin binding / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PHOSPHATE ION / Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGiardina, G. / Boumis, G. / Di Matteo, A. / Breccia, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)MX-2363European Union
CitationJournal: To Be Published
Title: Structural and functional defects of mitochondrial serine hydroxymethyltransferase genetic variants responsible for a novel neurodevelopmental syndrome
Authors: Giardina, G. / Boumis, G. / Di Matteo, A. / Breccia, S.
History
DepositionJul 12, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine hydroxymethyltransferase, mitochondrial
B: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2444
Polymers108,0542
Non-polymers1902
Water54030
1
A: Serine hydroxymethyltransferase, mitochondrial
B: Serine hydroxymethyltransferase, mitochondrial
hetero molecules

A: Serine hydroxymethyltransferase, mitochondrial
B: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,4898
Polymers216,1094
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)162.134, 162.134, 207.382
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A1_
21B4_
12A3_
22B6_

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRPLEULEUAA43 - 25825 - 240
21TRPTRPLEULEUBB43 - 25825 - 240
12ALAALAALAALAAA260 - 483242 - 465
22ALAALAALAALABB260 - 483242 - 465

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.924275, 0.18254, 0.335255), (0.167141, -0.596068, 0.785345), (0.343191, 0.781909, 0.520421)24.15388, 108.13322, -61.27567

-
Components

#1: Protein Serine hydroxymethyltransferase, mitochondrial / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 54027.176 Da / Num. of mol.: 2 / Mutation: P157S
Source method: isolated from a genetically manipulated source
Details: crystallized construct: SHMT2 Isoform 3 differences from canonical isoform: 1-21 missing and additional residues (GSH) at the N-ter belonging to cleaved His-tag
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34897, glycine hydroxymethyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: MORPHEUS screen (Molecular Dimensions) condition C4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.0596 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0596 Å / Relative weight: 1
ReflectionResolution: 2.7→140.41 Å / Num. obs: 44777 / % possible obs: 100 % / Redundancy: 21.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.202 / Net I/σ(I): 14.2
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 2.093 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4610 / CC1/2: 0.722

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→140.41 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.716 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.467 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25943 2296 5.1 %RANDOM
Rwork0.2546 ---
obs0.25485 42416 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.094 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20.66 Å20 Å2
2--1.32 Å2-0 Å2
3----4.27 Å2
Refinement stepCycle: 1 / Resolution: 2.7→140.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6741 0 10 30 6781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0126888
X-RAY DIFFRACTIONr_bond_other_d0.0030.0166526
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.6559333
X-RAY DIFFRACTIONr_angle_other_deg0.3321.57414965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.018565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42101125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0420.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028243
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021623
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0976.7483473
X-RAY DIFFRACTIONr_mcbond_other3.0966.7483473
X-RAY DIFFRACTIONr_mcangle_it4.94312.1124329
X-RAY DIFFRACTIONr_mcangle_other4.94312.1124330
X-RAY DIFFRACTIONr_scbond_it3.0737.0913415
X-RAY DIFFRACTIONr_scbond_other3.0647.0943408
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2412.9014993
X-RAY DIFFRACTIONr_long_range_B_refined7.99863.157929
X-RAY DIFFRACTIONr_long_range_B_other7.99863.167930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDNumberRms dev position (Å)
11171011.1
22159615.67
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 169 -
Rwork0.358 3076 -
obs--100 %

+
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