[English] 日本語
Yorodumi
- PDB-1li1: The 1.9-A crystal structure of the noncollagenous (NC1) domain of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1li1
TitleThe 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link
Components
  • Collagen alpha 1(IV)
  • Collagen alpha 2(IV)
KeywordsSTRUCTURAL PROTEIN / basement membrane / collagen IV / NC1 domain / covalent cross-link / protein-protein interaction
Function / homology
Function and homology information


collagen type IV trimer / retinal blood vessel morphogenesis / Anchoring fibril formation / Crosslinking of collagen fibrils / renal tubule morphogenesis / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / Extracellular matrix organization / basement membrane organization ...collagen type IV trimer / retinal blood vessel morphogenesis / Anchoring fibril formation / Crosslinking of collagen fibrils / renal tubule morphogenesis / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / Extracellular matrix organization / basement membrane organization / Collagen biosynthesis and modifying enzymes / collagen-activated tyrosine kinase receptor signaling pathway / Laminin interactions / Signaling by PDGF / NCAM1 interactions / blood vessel morphogenesis / Assembly of collagen fibrils and other multimeric structures / extracellular matrix structural constituent / Scavenging by Class A Receptors / neuromuscular junction development / branching involved in blood vessel morphogenesis / endodermal cell differentiation / Collagen degradation / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / epithelial cell differentiation / extracellular matrix organization / negative regulation of angiogenesis / response to activity / cellular response to amino acid stimulus / brain development / : / angiogenesis / molecular adaptor activity / endoplasmic reticulum lumen / DNA-templated transcription / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Noncollagenous (NC1) domain of collagen IV / Collagen IV, non-collagenous / Collagen IV, non-collagenous / Collagen IV, non-collagenous domain superfamily / C-terminal tandem repeated domain in type 4 procollagen / Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. / C-terminal tandem repeated domain in type 4 procollagens / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) ...Noncollagenous (NC1) domain of collagen IV / Collagen IV, non-collagenous / Collagen IV, non-collagenous / Collagen IV, non-collagenous domain superfamily / C-terminal tandem repeated domain in type 4 procollagen / Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. / C-terminal tandem repeated domain in type 4 procollagens / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin fold / Beta Complex / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Collagen alpha-1(IV) chain / Collagen alpha-2(IV) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsThan, M.E. / Henrich, S. / Huber, R. / Ries, A. / Mann, K. / Kuhn, K. / Timpl, R. / Bourenkov, G.P. / Bartunik, H.D. / Bode, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link.
Authors: Than, M.E. / Henrich, S. / Huber, R. / Ries, A. / Mann, K. / Kuhn, K. / Timpl, R. / Bourenkov, G.P. / Bartunik, H.D. / Bode, W.
History
DepositionApr 17, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Collagen alpha 1(IV)
B: Collagen alpha 1(IV)
C: Collagen alpha 2(IV)
D: Collagen alpha 1(IV)
E: Collagen alpha 1(IV)
F: Collagen alpha 2(IV)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,18815
Polymers151,6576
Non-polymers5319
Water20,0691114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38270 Å2
ΔGint-198 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.589, 234.589, 99.492
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological relevant hexamer [alpha 1(IV)]4, [alpha 2(IV)]2 corresponds to the asymmetric unit of this pdb entry.

-
Components

#1: Protein
Collagen alpha 1(IV)


Mass: 25356.871 Da / Num. of mol.: 4 / Fragment: noncollagenous domain 1 / Source method: isolated from a natural source / Details: placenta / Source: (natural) Homo sapiens (human) / References: UniProt: P02462
#2: Protein Collagen alpha 2(IV)


Mass: 25114.551 Da / Num. of mol.: 2 / Fragment: noncollagenous domain 1 / Source method: isolated from a natural source / Details: placenta / Source: (natural) Homo sapiens (human) / References: UniProt: P08572
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1114 / 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: 3.47 Å3/Da / Density % sol: 64.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: MES, sodium acetate, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 7.5 / PH range high: 7.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
220 mM1dropNH4HCO3
30.1 MMES-NaOH1reservoir
43.2-3.6 Msodium acetate1reservoirpH7.1-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2001 / Details: mirror
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.9→19.95 Å / Num. obs: 155867 / % possible obs: 96.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 34.9 Å2
Reflection shellResolution: 1.9→2 Å / % possible all: 97.6
Reflection
*PLUS
Num. measured all: 441349 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.3

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→19.95 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.202 7569 5.1 %RANDOM
Rwork0.182 ---
obs0.182 148362 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.4937 Å2 / ksol: 0.351246 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.1 Å2-2.88 Å2-
2---7.1 Å2-
3---14.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10514 0 36 1114 11664
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.842
X-RAY DIFFRACTIONc_scangle_it3.852.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 1340 5.2 %
Rwork0.277 24252 -
obs--95.3 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
LS refinement shell
*PLUS
Rfactor obs: 0.277

+
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