[English] 日本語
Yorodumi
- PDB-9w5z: Structure of heme transport protein Shr-Linker-NEAT1 from Strepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9w5z
TitleStructure of heme transport protein Shr-Linker-NEAT1 from Streptococcus pyogenes in complex with heme.
ComponentsStreptococcal hemoprotein receptor
KeywordsMETAL TRANSPORT / Heme binding Shr Streptococcus pyogenes Iron acquisition Antimicrobial strategy Heme transfer
Function / homology
Function and homology information


peptidoglycan-based cell wall / metal ion binding / plasma membrane
Similarity search - Function
Heme-binding protein Shr-like, Hb-interacting domain / Heme-binding protein Shr-like, Hb-interacting domain / : / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat ...Heme-binding protein Shr-like, Hb-interacting domain / Heme-binding protein Shr-like, Hb-interacting domain / : / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Streptococcal hemoprotein receptor
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSenoo, A. / Caaveiro, J.M.M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K18262 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121031 Japan
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Structural basis for heme binding by the Shr protein from Streptococcus pyogenes.
Authors: Seki, K. / Senoo, A. / Nagatoishi, S. / Yanaka, S. / Nakakido, M. / Tsumoto, K. / Caaveiro, J.M.M.
History
DepositionAug 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Streptococcal hemoprotein receptor
B: Streptococcal hemoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7915
Polymers46,3492
Non-polymers1,4423
Water1,27971
1
A: Streptococcal hemoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7912
Polymers23,1741
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-18 kcal/mol
Surface area11810 Å2
MethodPISA
2
B: Streptococcal hemoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0003
Polymers23,1741
Non-polymers8262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.585, 113.246, 44.281
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Streptococcal hemoprotein receptor / Heme-acquisition protein Shr / Heme-binding protein Shr / Hemoprotein binding receptor


Mass: 23174.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: shr, SPy_1798 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99YA0
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 200 mM NaCl 100 mM BIS-TRIS 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→42.32 Å / Num. obs: 17354 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.055 / Net I/σ(I): 11
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1669 / CC1/2: 0.865 / Rpim(I) all: 0.277 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
XDS20241002data reduction
Aimless0.8.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→42.32 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.816 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26417 861 5 %RANDOM
Rwork0.21579 ---
obs0.21821 16477 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.056 Å2
Baniso -1Baniso -2Baniso -3
1-32.99 Å20 Å2-6.6 Å2
2---10.3 Å2-0 Å2
3----22.69 Å2
Refinement stepCycle: 1 / Resolution: 2.35→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 100 71 3355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123339
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163232
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.8974513
X-RAY DIFFRACTIONr_angle_other_deg0.4351.7987489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1515411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.433528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56310650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0530.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02657
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_it2.3643.7241638
X-RAY DIFFRACTIONr_mcbond_other2.3643.7241638
X-RAY DIFFRACTIONr_mcangle_it3.6796.6842045
X-RAY DIFFRACTIONr_mcangle_other3.6796.6852046
X-RAY DIFFRACTIONr_scbond_it2.7274.0351701
X-RAY DIFFRACTIONr_scbond_other2.7264.0351702
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5327.2992467
X-RAY DIFFRACTIONr_long_range_B_refined6.2138.633634
X-RAY DIFFRACTIONr_long_range_B_other6.21238.643631
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 57 -
Rwork0.268 1207 -
obs--98.98 %

+
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