[English] 日本語
Yorodumi
- PDB-2ria: Crystal structure of the trimeric neck and carbohydrate recogniti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ria
TitleCrystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose
ComponentsPulmonary surfactant-associated protein D
KeywordsSUGAR BINDING PROTEIN / SURFACTANT PROTEIN / CARBOHYDRATE RECOGNITION / DOMAIN TRIMERIC
Function / homology
Function and homology information


Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / extracellular matrix structural constituent conferring tensile strength / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer ...Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / extracellular matrix structural constituent conferring tensile strength / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer / surfactant homeostasis / Signal regulatory protein family interactions / negative regulation of interleukin-2 production / lung alveolus development / macrophage chemotaxis / endocytic vesicle / negative regulation of T cell proliferation / positive regulation of phagocytosis / regulation of cytokine production / multivesicular body / reactive oxygen species metabolic process / extracellular matrix organization / receptor-mediated endocytosis / SARS-CoV-1 activates/modulates innate immune responses / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / carbohydrate binding / collagen-containing extracellular matrix / lysosome / defense response to bacterium / innate immune response / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / Collectin, C-type lectin-like domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain ...Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / Collectin, C-type lectin-like domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
D-glycero-alpha-D-manno-heptopyranose / Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsWang, H. / Head, J. / Kosma, P. / Sheikh, S. / McDonald, B. / Smith, K. / Cafarella, T. / Seaton, B. / Crouch, E.
CitationJournal: Biochemistry / Year: 2008
Title: Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d.
Authors: Wang, H. / Head, J. / Kosma, P. / Brade, H. / Muller-Loennies, S. / Sheikh, S. / McDonald, B. / Smith, K. / Cafarella, T. / Seaton, B. / Crouch, E.
History
DepositionOct 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pulmonary surfactant-associated protein D
B: Pulmonary surfactant-associated protein D
C: Pulmonary surfactant-associated protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,80815
Polymers51,8173
Non-polymers99112
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.414, 108.606, 55.548
Angle α, β, γ (deg.)90.000, 91.030, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Pulmonary surfactant-associated protein D / SP-D / PSP-D / Lung surfactant protein D


Mass: 17272.209 Da / Num. of mol.: 3 / Fragment: neck and carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD, PSPD, SFTP4 / Plasmid: PET30A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTABLUE / References: UniProt: P35247
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-289 / D-glycero-alpha-D-manno-heptopyranose


Type: D-saccharide, alpha linking / Mass: 210.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H14O7
IdentifierTypeProgram
D-gro-a-D-manHeppIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
DDmanHepSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 58216 / % possible obs: 95.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.069 / Χ2: 1.164 / Net I/σ(I): 23.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.842.40.33237741.03192.6
1.84-1.892.40.26138061.02795.6
1.89-1.942.50.20239031.00896
1.94-22.50.16438881.04295.7
2-2.062.50.13438701.05295.9
2.06-2.132.60.11239421.11596.7
2.13-2.222.50.09739271.05997.2
2.22-2.322.60.08839321.1597.6
2.32-2.442.60.07939401.17597.7
2.44-2.62.70.07439751.24697.6
2.6-2.82.80.06939681.18497.7
2.8-3.082.80.06338791.21596
3.08-3.522.90.06138691.33994.7
3.52-4.442.90.05938101.29893.7
4.44-5030.06337331.33989.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / FOM work R set: 0.856 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.237 5845 9.6 %
Rwork0.209 --
obs-57372 94.4 %
Solvent computationBsol: 50.289 Å2
Displacement parametersBiso mean: 26.903 Å2
Baniso -1Baniso -2Baniso -3
1-0.266 Å20 Å20.577 Å2
2---2.792 Å20 Å2
3---2.526 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 51 378 3774
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1447
X-RAY DIFFRACTIONc_bond_d0.0053
X-RAY DIFFRACTIONc_mcbond_it1.2021.5
X-RAY DIFFRACTIONc_mcangle_it1.7732
X-RAY DIFFRACTIONc_scbond_it2.0132
X-RAY DIFFRACTIONc_scangle_it2.9492.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4ddh1.par

+
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://pdbjlvh1.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