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- EMDB-44397: Full-length cross-linked Contactin 2 (FN1 apart) -

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Basic information

Entry
Database: EMDB / ID: EMD-44397
TitleFull-length cross-linked Contactin 2 (FN1 apart)
Map data
Sample
  • Organelle or cellular component: Contactin-2 full length (Ig1-FN4)
    • Protein or peptide: Contactin 2 (full-length)
Keywordscontactins / adhesion molecule / protein structure / conformational changes / homodimer / MEMBRANE PROTEIN
Function / homology
Function and homology information


establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / reduction of food intake in response to dietary excess / L1CAM interactions / clustering of voltage-gated potassium channels / protein localization to juxtaparanode region of axon / dendrite self-avoidance / NrCAM interactions / cell-cell adhesion mediator activity / axon initial segment ...establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / reduction of food intake in response to dietary excess / L1CAM interactions / clustering of voltage-gated potassium channels / protein localization to juxtaparanode region of axon / dendrite self-avoidance / NrCAM interactions / cell-cell adhesion mediator activity / axon initial segment / node of Ranvier / juxtaparanode region of axon / NCAM1 interactions / fat cell differentiation / homophilic cell adhesion via plasma membrane adhesion molecules / side of membrane / synapse organization / axon guidance / brain development / myelin sheath / postsynaptic membrane / cell adhesion / axon / synapse / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III ...: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsLiu JL / Fan SF / Ren GR / Rudenko GR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) United States
CitationJournal: To Be Published
Title: Molecular mechanism of Contactin 2 homophilic interaction
Authors: Fan SF / Liu JL / Chofflett NC / Bailey AB / Russell WR / Zhang ZZ / Takahashi HT / Ren GR / Rudenko GR
History
DepositionApr 3, 2024-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44397.png

Downloads & links

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Map

FileDownload / File: emd_44397.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.018600551 - 2.091152
Average (Standard dev.)0.00053162023 (±0.013535566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44397_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44397_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Contactin-2 full length (Ig1-FN4)

EntireName: Contactin-2 full length (Ig1-FN4)
Components
  • Organelle or cellular component: Contactin-2 full length (Ig1-FN4)
    • Protein or peptide: Contactin 2 (full-length)

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Supramolecule #1: Contactin-2 full length (Ig1-FN4)

SupramoleculeName: Contactin-2 full length (Ig1-FN4) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Contactin 2 (full-length)

MacromoleculeName: Contactin 2 (full-length) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ELGTGLE SQ TTFGPVFE D QPLSVLFPE ESTEEQVLLA CRARASPPA T YRWKMNGT EM KLEPGSR HQL VGGNLV IMNP TKAQD AGVYQ CLAS NPVGTV VSR EAILRFG FL QEFSKEER D PVKAHEGWG VMLPCNPPAH YPGLSYRWL L NEFPNFIP TD ...String:
ELGTGLE SQ TTFGPVFE D QPLSVLFPE ESTEEQVLLA CRARASPPA T YRWKMNGT EM KLEPGSR HQL VGGNLV IMNP TKAQD AGVYQ CLAS NPVGTV VSR EAILRFG FL QEFSKEER D PVKAHEGWG VMLPCNPPAH YPGLSYRWL L NEFPNFIP TD GRHFVSQ TTG NLYIAR TNAS DLGNY SCLAT SHMD FSTKSV FSK FAQLNLA AE DTRLFAPS I KARFPAETY ALVGQQVTLE CFAFGNPVP R IKWRKVDG SL SPQWTTA EPT LQIPSV SFED EGTYE CEAEN SKGR DTVQGR IIV QAQPEWL KV ISDTEADI G SNLRWGCAA AGKPRPTVRW LRNGEPLAS Q NRVEVLAG DL RFSKLSL EDS GMYQCV AENK HGTIY ASAEL AVQA LAPDFR LNP VRRLIPA AR GGEILIPC Q PRAAPKAVV LWSKGTEILV NSSRVTVTP D GTLIIRNI SR SDEGKYT CFA ENFMGK ANST GILSV RDATK ITLA PSSADI NLG DNLTLQC HA SHDPTMDL T FTWTLDDFP IDFDKPGGHY RRTNVKETI G DLTILNAQ LR HGGKYTC MAQ TVVDSA SKEA TVLVR GPPGP PGGV VVRDIG DTT IQLSWSR GF DNHSPIAK Y TLQARTPPA GKWKQVRTNP ANIEGNAET A QVLGLTPW MD YEFRVIA SNI LGTGEP SGPS SKIRT REAAP SVAP SGLSGG GGA PGELIVN WT PMSREYQN G DGFGYLLSF RRQGSTHWQT ARVPGADAQ Y FVYSNESV RP YTPFEVK IRS YNRRGD GPES LTALV YSAEE EPRV APTKVW AKG VSSSEMN VT WEPVQQDM N GILLGYEIR YWKAGDKEAA ADRVRTAGL D TSARVSGL HP NTKYHVT VRA YNRAGT GPAS PSANA TTMKP PPRR PPGNIS WTF SSSSLSI KW DPVVPFRN E SAVTGYKML YQNDLHLTPT LHLTGKNWI E IPVPEDIG HA LVQIRTT GPG GDGIPA EVHI VRN G SASTSHHHHH H

UniProtKB: Contactin-2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
10.0 mMHEPES
50.0 mMSodium chlorideNaCl

Details: 10 mM HEPES pH 8.0, 50 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9049 / Average exposure time: 7.39 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Details: The initial volume was generated by ab initio reconstruction.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.0) / Number images used: 78918
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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