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- PDB-7oqz: Cryo-EM structure of human TMEM45A -

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Basic information

Entry
Database: PDB / ID: 7oqz
TitleCryo-EM structure of human TMEM45A
ComponentsTransmembrane protein 45ATransmembrane protein
KeywordsMEMBRANE PROTEIN / Transmembrane Protein 45A
Function / homologyProtein of unknown function DUF716 / Transmembrane protein 45 / Family of unknown function (DUF716) / membrane => GO:0016020 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Transmembrane protein 45A
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsGrieben, M. / Pike, A.C.W. / Evans, A. / Shrestha, L. / Venkaya, S. / Mukhopadhyay, S.M.M. / Moreira, T. / Chalk, R. / MacLean, E.M. / Marsden, B.D. ...Grieben, M. / Pike, A.C.W. / Evans, A. / Shrestha, L. / Venkaya, S. / Mukhopadhyay, S.M.M. / Moreira, T. / Chalk, R. / MacLean, E.M. / Marsden, B.D. / Burgess-Brown, N.A. / Bountra, C. / Carpenter, E.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
European Commission115766 United Kingdom
CitationJournal: To Be Published
Title: CryoEM structure of human TMEM45A
Authors: Grieben, M. / Pike, A.C.W. / Evans, A. / Shrestha, L. / Venkaya, S. / Mukhopadhyay, S.M.M. / Moreira, T. / Marsden, B.D. / Burgess-Brown, N.A. / Carpenter, E.P.
History
DepositionJun 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Other / Structure summary
Category: audit_author / citation ...audit_author / citation / pdbx_SG_project / struct_keywords
Item: _citation.title / _struct_keywords.text

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Transmembrane protein 45A
B: Transmembrane protein 45A
C: Transmembrane protein 45A
D: Transmembrane protein 45A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,71620
Polymers130,0734
Non-polymers12,64216
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25460 Å2
ΔGint-259 kcal/mol
Surface area42330 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNLEUA1 - 237
d_12ens_1PC1PC1B
d_13ens_1PC1PC1C
d_14ens_1PC1PC1D
d_15ens_1PC1PC1E
d_21ens_1ASNLEUF1 - 237
d_22ens_1PC1PC1G
d_23ens_1PC1PC1H
d_24ens_1PC1PC1I
d_25ens_1PC1PC1J
d_31ens_1ASNLEUK1 - 237
d_32ens_1PC1PC1L
d_33ens_1PC1PC1M
d_34ens_1PC1PC1N
d_35ens_1PC1PC1O
d_41ens_1ASNLEUP1 - 237
d_42ens_1PC1PC1Q
d_43ens_1PC1PC1R
d_44ens_1PC1PC1S
d_45ens_1PC1PC1T

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Components

#1: Protein
Transmembrane protein 45A / Transmembrane protein / DNA polymerase-transactivated protein 4 / Dermal papilla-derived protein 7


Mass: 32518.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM45A, DERP7, DNAPTP4 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NWC5
#2: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Transmembrane Protein 45ATransmembrane protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45.9 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionDetails: Patch CTF routine in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94268 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 129.04 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00188216
ELECTRON MICROSCOPYf_angle_d0.340111068
ELECTRON MICROSCOPYf_chiral_restr0.03081220
ELECTRON MICROSCOPYf_plane_restr0.0031288
ELECTRON MICROSCOPYf_dihedral_angle_d10.43572976
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000698191197779
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.081569546592
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000699454035062

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