[English] 日本語
Yorodumi
- PDB-2yad: BRICHOS domain of Surfactant protein C precursor protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yad
TitleBRICHOS domain of Surfactant protein C precursor protein
ComponentsSURFACTANT PROTEIN C BRICHOS DOMAIN
KeywordsSURFACTANT PROTEIN / PULMONARY SURFACTANT SYSTEM / INTERSTITIAL LUNG DISEASE / AMYLOID / CHAPERONE
Function / homology
Function and homology information


Defective pro-SFTPC causes SMDP2 and RDS / multivesicular body lumen / lamellar body / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Surfactant metabolism / endoplasmic reticulum membrane ...Defective pro-SFTPC causes SMDP2 and RDS / multivesicular body lumen / lamellar body / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Surfactant metabolism / endoplasmic reticulum membrane / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Enolase-like; domain 1 - #150 / Pulmonary surfactant-associated protein C / Pulmonary surfactant proteins / Surfactant-associated polypeptide, palmitoylation site / Surfactant associated polypeptide SP-C palmitoylation sites. / Surfactant protein C, N-terminal propeptide / Surfactant protein C, N terminal propeptide / BRICHOS / BRICHOS domain / BRICHOS domain ...Enolase-like; domain 1 - #150 / Pulmonary surfactant-associated protein C / Pulmonary surfactant proteins / Surfactant-associated polypeptide, palmitoylation site / Surfactant associated polypeptide SP-C palmitoylation sites. / Surfactant protein C, N-terminal propeptide / Surfactant protein C, N terminal propeptide / BRICHOS / BRICHOS domain / BRICHOS domain / BRICHOS domain profile. / Enolase-like; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Surfactant protein C / Surfactant protein C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsAskarieh, G. / Siponen, M.I. / Willander, H. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. ...Askarieh, G. / Siponen, M.I. / Willander, H. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. / Bergman, T. / Saenz, A. / Casals, C. / Aqvist, J. / Jornvall, H. / Presto, J. / Johansson, J. / Arrowsmith, C.H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Nordlund, P. / Persson, C. / Schuler, H. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Berglund, H. / Knight, S.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: High Resolution Structure of a Bricos Domain and its Implications for Anti-Amyloid Chaperone Activity on Lung Surgactant Protein C.
Authors: Willander, H. / Askarieh, G. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. / Bergman, T. / Saenz, A. / Casals, C. / Aqvist, J. / ...Authors: Willander, H. / Askarieh, G. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. / Bergman, T. / Saenz, A. / Casals, C. / Aqvist, J. / Jornvall, H. / Berglund, H. / Presto, J. / Knight, S.D. / Johansson, J.
History
DepositionFeb 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Other
Revision 1.2Aug 13, 2014Group: Refinement description
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SURFACTANT PROTEIN C BRICHOS DOMAIN
B: SURFACTANT PROTEIN C BRICHOS DOMAIN
C: SURFACTANT PROTEIN C BRICHOS DOMAIN
D: SURFACTANT PROTEIN C BRICHOS DOMAIN
E: SURFACTANT PROTEIN C BRICHOS DOMAIN
F: SURFACTANT PROTEIN C BRICHOS DOMAIN


Theoretical massNumber of molelcules
Total (without water)112,2536
Polymers112,2536
Non-polymers00
Water1,874104
1
A: SURFACTANT PROTEIN C BRICHOS DOMAIN
B: SURFACTANT PROTEIN C BRICHOS DOMAIN
E: SURFACTANT PROTEIN C BRICHOS DOMAIN


Theoretical massNumber of molelcules
Total (without water)56,1273
Polymers56,1273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-19.6 kcal/mol
Surface area10770 Å2
MethodPISA
2
C: SURFACTANT PROTEIN C BRICHOS DOMAIN
D: SURFACTANT PROTEIN C BRICHOS DOMAIN
F: SURFACTANT PROTEIN C BRICHOS DOMAIN


Theoretical massNumber of molelcules
Total (without water)56,1273
Polymers56,1273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-21.5 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.046, 39.329, 114.756
Angle α, β, γ (deg.)90.00, 99.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-139-

ARG

-
Components

#1: Protein
SURFACTANT PROTEIN C BRICHOS DOMAIN


Mass: 18708.883 Da / Num. of mol.: 6 / Fragment: RESIDUES 15-144
Source method: isolated from a genetically manipulated source
Details: EXPRESSED N-TERMINAL SEQUENCE DIFFERS FROM UNIPROT REFERENCE
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI B(DE3) / Variant (production host): PLYSS / References: UniProt: E5RI64, UniProt: P11686*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE EXPRESSED PROTEIN DIFFERS FROM THE UNIPROT REFERENCE SEQUENCE AT THE N-TERMINUS. THE SEQUENCE ...THE EXPRESSED PROTEIN DIFFERS FROM THE UNIPROT REFERENCE SEQUENCE AT THE N-TERMINUS. THE SEQUENCE HMSQKHTEM IS PART OF PROTEIN AND NOT THE EXPRESSION TAG. DATABASE REFERENCE FOR THE EXPRESSED PROTEIN IS NCBI REFERENCE NP_003009.2. WITH TRUNCATION OF FIRST 58 RESIDUES AND S-TAG REMOVED BY IN SITU PROTEOLYSIS DURING CRYSTALLIZATION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.32 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97925
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 34299 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 37.52 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.1

-
Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.2→27.43 Å / Cor.coef. Fo:Fc: 0.9366 / Cor.coef. Fo:Fc free: 0.9078 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IN SITU PROTEOLYSIS. UNSTRUCTURED LOOP BETWEEN HELIX 1 AND HELIX 2 AS WELL AS THE N-TERMINAL S-TAG AND LINKER ARE FULLY OR PARTLY CLEAVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1476 5.09 %RANDOM
Rwork0.1902 ---
obs0.1918 29015 --
Displacement parametersBiso mean: 46.33 Å2
Baniso -1Baniso -2Baniso -3
1-6.7617 Å20 Å22.4415 Å2
2---11.1612 Å20 Å2
3---4.3994 Å2
Refine analyzeLuzzati coordinate error obs: 0.324 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 0 104 3599
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013687HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.075050HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1616SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes544HARMONIC5
X-RAY DIFFRACTIONt_it3687HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion2.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion523SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4285SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.183 96 4.43 %
Rwork0.1968 2070 -
all0.1962 2166 -
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)
17.7502-1.45321.43220.14430.3147.2124-0.1863-0.91490.65730.1159-0.0078-0.1043-0.4228-0.31170.194-0.07560.0416-0.06360.1052-0.0932-0.149146.994910.993844.1835
24.8662-0.74041.238900.76085.07080.0340.28540.0867-0.1972-0.1045-0.03-0.2180.58240.0705-0.09750.02270.00490.08310.0163-0.095451.80075.184324.0876
32.9928-1.17150.5881.22510.37044.0375-0.0399-0.02160.0269-0.00740.0489-0.0090.0361-0.0207-0.0090.0066-0.02940.0086-0.07570.0053-0.054629.99796.02768.7869
45.251-1.46140.69470.24610.9034.7957-0.0923-0.82030.290.0579-0.01240.0606-0.5426-0.45270.1047-0.07780.1347-0.03590.1009-0.1093-0.096825.394214.232128.0482
57.0077-0.08851.37810.77671.96188.6358-0.07020.16280.3241-0.1347-0.0309-0.193-0.32381.13160.1012-0.1783-0.0050.01470.2687-0.0092-0.197967.35476.610939.1877
65.2674-1.1904-0.06831.60931.91735.8157-0.1169-0.16190.3212-0.23-0.17490.1841-0.5322-0.7930.2918-0.10930.1759-0.03270.1348-0.0941-0.108410.449415.406312.665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A90 - A149 OR A181 - A197)
2X-RAY DIFFRACTION2(B89 - B149 OR B180 - B197)
3X-RAY DIFFRACTION3(C87 - C151 OR C180 - C197)
4X-RAY DIFFRACTION4(D88 - D148 OR D180 - D197)
5X-RAY DIFFRACTION5(E89 - E149 OR E180 - E197)
6X-RAY DIFFRACTION6(F89 - F148 OR F181 - F197)

+
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