[English] 日本語
Yorodumi
- PDB-7b4l: CryoEM structure of the human sodium proton exchanger NHA2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b4l
TitleCryoEM structure of the human sodium proton exchanger NHA2
ComponentsSodium/hydrogen exchanger 9B2
KeywordsMEMBRANE PROTEIN / secondary active transporter / membrane transport / ion antiport / pH regulation
Function / homology
Function and homology information


lithium:proton antiporter activity / lithium ion transport / positive regulation of osteoclast development / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / flagellated sperm motility / : ...lithium:proton antiporter activity / lithium ion transport / positive regulation of osteoclast development / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / flagellated sperm motility / : / sodium ion transport / recycling endosome / mitochondrial membrane / Stimuli-sensing channels / recycling endosome membrane / synaptic vesicle membrane / monoatomic ion transmembrane transport / basolateral plasma membrane / mitochondrial inner membrane / apical plasma membrane / mitochondrion / identical protein binding / plasma membrane
Similarity search - Function
: / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane
Similarity search - Domain/homology
TETRADECANE / Chem-POV / UNDECANE / Sodium/hydrogen exchanger 9B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWoehlert, D. / Kuhlbrandt, W. / Yildiz, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB807 Germany
CitationJournal: To Be Published
Title: CryoEM structure of the human sodium proton exchanger NHA2
Authors: Woehlert, D. / Kuhlbrandt, W. / Yildiz, O.
History
DepositionDec 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12002
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sodium/hydrogen exchanger 9B2
B: Sodium/hydrogen exchanger 9B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,06324
Polymers115,2232
Non-polymers5,84022
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area13260 Å2
ΔGint-42 kcal/mol
Surface area35920 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLUN1 - 443
d_12ens_1NANAO
d_13ens_1POVPOVP
d_14ens_1POVPOVQ
d_15ens_1C14C14R
d_16ens_1C14C14S
d_17ens_1C14C14T
d_18ens_1UNDUNDU
d_19ens_1UNDUNDV
d_110ens_1UNDUNDW
d_111ens_1UNDUNDX
d_112ens_1UNDUNDY
d_21ens_1PROGLUA1 - 443
d_22ens_1NANAB
d_23ens_1POVPOVC
d_24ens_1POVPOVD
d_25ens_1C14C14E
d_26ens_1C14C14F
d_27ens_1C14C14G
d_28ens_1UNDUNDH
d_29ens_1UNDUNDI
d_210ens_1UNDUNDJ
d_211ens_1UNDUNDK
d_212ens_1UNDUNDL

NCS oper: (Code: givenMatrix: (-0.999999999982, 5.59715458854E-6, 1.92899463423E-6), (-5.59715564979E-6, -0.999999999984, -5.5014751263E-7), (1.92899155494E-6, -5.50158309504E-7, 0.999999999998) ...NCS oper: (Code: given
Matrix: (-0.999999999982, 5.59715458854E-6, 1.92899463423E-6), (-5.59715564979E-6, -0.999999999984, -5.5014751263E-7), (1.92899155494E-6, -5.50158309504E-7, 0.999999999998)
Vector: 96.5695181285, 92.2782140751, -3.16066012402E-5)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Sodium/hydrogen exchanger 9B2 / Na(+)/H(+) exchanger NHA2 / Na(+)/H(+) exchanger-like domain-containing protein 2 / NHE domain- ...Na(+)/H(+) exchanger NHA2 / Na(+)/H(+) exchanger-like domain-containing protein 2 / NHE domain-containing protein 2 / Sodium/hydrogen exchanger-like domain-containing protein 2 / Solute carrier family 9 subfamily B member 2


Mass: 57611.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9B2, NHA2, NHEDC2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q86UD5

-
Non-polymers , 5 types, 48 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#4: Chemical
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H30
#5: Chemical
ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C11H24
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human sodium proton exchanger NHA2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4326

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2243669
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165793 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 57.82 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00257122
ELECTRON MICROSCOPYf_angle_d0.53499572
ELECTRON MICROSCOPYf_chiral_restr0.03811146
ELECTRON MICROSCOPYf_plane_restr0.0051122
ELECTRON MICROSCOPYf_dihedral_angle_d21.41751212
Refine LS restraints NCSType: NCS constraints / Rms dev position: 0.000383998782733 Å

+
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