[English] 日本語
Yorodumi
- PDB-9z0m: Human CD300c extracellular domain pH 7.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9z0m
TitleHuman CD300c extracellular domain pH 7.5
ComponentsCMRF35-like molecule 6
KeywordsIMMUNE SYSTEM / CD300c / IGV-like domain / lipid binding protein / myeloid receptor / CMRF-35-like molecule-6 / CLM-6 / CMRF-35 / CMRF35-A1 / IgSF16
Function / homology
Function and homology information


regulation of innate immune response / immune system process / cellular defense response / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
CMRF35-like molecule 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTennant, L. / Littler, D.R. / Rossjohn, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Ligand recognition in the CD300c extracellular domain
Authors: Tennant, L. / Littler, D.R. / Rossjohn, J.
History
DepositionNov 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CMRF35-like molecule 6


Theoretical massNumber of molelcules
Total (without water)12,5791
Polymers12,5791
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.329, 38.207, 82.366
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein CMRF35-like molecule 6 / CLM-6 / CD300 antigen-like family member C / CMRF35-A1 / CMRF-35 / Immunoglobulin superfamily ...CLM-6 / CD300 antigen-like family member C / CMRF35-A1 / CMRF-35 / Immunoglobulin superfamily member 16 / IgSF16


Mass: 12579.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD300C, CMRF35, CMRF35A, CMRF35A1, IGSF16 / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q08708
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG1500, 0.1 M HEPES, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.7→41.18 Å / Num. obs: 11124 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 28.37 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 14.7
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 574 / CC1/2: 0.459 / Rpim(I) all: 0.669

-
Processing

Software
NameVersionClassification
PHENIX2.0_5761refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.18 Å / SU ML: 0.1459 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9241
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2393 556 5.01 %
Rwork0.2017 10534 -
obs0.2036 11090 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 0 49 904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075879
X-RAY DIFFRACTIONf_angle_d0.97321196
X-RAY DIFFRACTIONf_chiral_restr0.0595130
X-RAY DIFFRACTIONf_plane_restr0.0075155
X-RAY DIFFRACTIONf_dihedral_angle_d18.3126324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.870.25781300.25152579X-RAY DIFFRACTION100
1.87-2.140.3091460.21642576X-RAY DIFFRACTION100
2.14-2.70.28731370.24412618X-RAY DIFFRACTION100
2.7-41.180.20731430.18072761X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.33091999677672.08481026900680.298535277346223.59617185371971.41498230001762.80163608404470.0247164109541320.019542918193027-0.57385115236743-0.846358932401450.075168219566004-0.598989396950890.0144577372673520.479066758320240.0652552783437780.490656748913740.0079174975989660.0463622882342370.393080038472350.218481161264290.23737864215204-13.310810972382.69381374515123.5414683414559
24.2407794645944-1.0982280889760.689949085486955.6378428572287-1.29455479710193.9318915374430.144790773325570.2998689491898-0.12455682455867-0.23368473627344-0.062562014990437-0.595483244617820.569380844641990.13404066092796-0.0684678607963260.285531388843640.019466353051242-0.021491593317080.2512724170905-0.0457926800881470.31168414234144-7.2554453218502-12.9964854978987.1268811583716
32.43174220475461.64432265428521.31674517328841.41767966537691.00701399572531.7335635028659-0.086056133594648-0.344446607761340.431595188823420.207217410258660.1151852967645-0.2548393653109-0.093375450740582-0.1275413217266-0.00800669402936640.24514307454030.015251183379665-0.0686238842019020.2625020568823-0.0487532310957360.29573138059435-9.0432311207341-3.108041737461418.855289314746
45.2554855919887-1.35525461789330.779639978723995.82366833000410.127428765954825.00397536900790.25396673803338-0.437029614669030.0221747317867190.31277907970868-0.39383020046072-0.0272194262006040.34569679065486-0.43923541610270.190083746816960.20618240121007-0.0777638518510060.037981771641380.35785542342580.0597797768788370.26677507340165-19.36443710682-8.149190005389517.093197156818
54.3989851149136-4.8637242234022-4.49463233180036.51130917756816.39154775057646.51236454321630.494106238524370.73696961705238-0.37594490397978-0.39220856323937-0.547960441612160.065347354030590.47099746986233-0.620988472607880.00670774271305120.332577584023410.015655296166835-0.0637584955367990.29162295104421-0.043536167765730.23976495228353-15.123156549667-13.0056962900387.7132368153497
62.6345403354412-1.09422269769481.47321963031123.7462852939284-1.40965156549843.1472744369158-0.0695624025996330.000538675203458010.229031997030590.19036360082370.057614180795175-0.2312441180815-0.26221226357634-0.248351437031190.0190820806959070.222460571227450.012890127435642-0.0248195848375490.23218270732225-0.00686968597217880.2440760007319-14.102215469456-1.045835328622810.356114097045
70.167481778303520.17792675751184-0.229030212205891.4640928852343-0.173804770398470.317105659241760.09840148896437-0.706938267326960.0616065033713410.391035848597720.038464897457247-0.530934480739740.032699951391790.12782038428298-0.105470050014630.338342706879150.038796112234111-0.13052717235510.424358566355590.0728920451083690.45160381105776-1.3390554663403-11.26253776546722.704376142368
86.1044590850706-5.12323353573121.58829714357488.2185609402545-1.32171220460924.64994046321630.182863284964120.832897039411650.56676696257827-0.67942280346694-0.15337516660555-0.3769475814818-0.678836978798930.126371574870560.0505411651258070.43643610518199-0.0406872046330690.055610133079680.35710120845220.0956485568548550.44296519648355-11.6821262123394.50210158742665.6035165603617
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 13 )2 - 131 - 12
22chain 'A' and (resid 14 through 27 )14 - 2713 - 26
33chain 'A' and (resid 28 through 45 )28 - 4527 - 44
44chain 'A' and (resid 46 through 56 )46 - 5645 - 55
55chain 'A' and (resid 57 through 65 )57 - 6556 - 64
66chain 'A' and (resid 66 through 88 )66 - 8865 - 87
77chain 'A' and (resid 89 through 97 )89 - 9788 - 96
88chain 'A' and (resid 98 through 110 )98 - 11097 - 109

+
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