[English] 日本語
Yorodumi
- PDB-1gnh: HUMAN C-REACTIVE PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gnh
TitleHUMAN C-REACTIVE PROTEIN
ComponentsC-REACTIVE PROTEIN
KeywordsACUTE-PHASE PROTEIN / PENTRAXIN / ACUTE-PHASE REACTANT
Function / homology
Function and homology information


regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / Classical antibody-mediated complement activation / low-density lipoprotein particle receptor binding / negative regulation of macrophage derived foam cell differentiation ...regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / Classical antibody-mediated complement activation / low-density lipoprotein particle receptor binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / positive regulation of superoxide anion generation / acute-phase response / defense response to Gram-positive bacterium / inflammatory response / innate immune response / calcium ion binding / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Pentaxin, conserved site / Pentraxin domain signature. / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsShrive, A.K. / Cheetham, G.M.T. / Holden, D. / Myles, D.A. / Turnell, W.G. / Volanakis, J.E. / Pepys, M.B. / Bloomer, A.C. / Greenhough, T.J.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: Three dimensional structure of human C-reactive protein.
Authors: Shrive, A.K. / Cheetham, G.M. / Holden, D. / Myles, D.A. / Turnell, W.G. / Volanakis, J.E. / Pepys, M.B. / Bloomer, A.C. / Greenhough, T.J.
History
DepositionMar 1, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-REACTIVE PROTEIN
B: C-REACTIVE PROTEIN
C: C-REACTIVE PROTEIN
D: C-REACTIVE PROTEIN
E: C-REACTIVE PROTEIN
F: C-REACTIVE PROTEIN
G: C-REACTIVE PROTEIN
H: C-REACTIVE PROTEIN
I: C-REACTIVE PROTEIN
J: C-REACTIVE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,32226
Polymers230,68010
Non-polymers64116
Water00
1
A: C-REACTIVE PROTEIN
B: C-REACTIVE PROTEIN
C: C-REACTIVE PROTEIN
D: C-REACTIVE PROTEIN
E: C-REACTIVE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,66113
Polymers115,3405
Non-polymers3218
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: C-REACTIVE PROTEIN
G: C-REACTIVE PROTEIN
H: C-REACTIVE PROTEIN
I: C-REACTIVE PROTEIN
J: C-REACTIVE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,66113
Polymers115,3405
Non-polymers3218
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.060, 154.250, 242.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
C-REACTIVE PROTEIN / HUMAN CRP HCRP


Mass: 23068.039 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02741
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
Compound detailsTHE SIDE CHAIN OF ASN 61 IN PROTOMERS C AND I (THE PROTOMERS WHERE THE 140 - 150 LOOP FROM D, J, ...THE SIDE CHAIN OF ASN 61 IN PROTOMERS C AND I (THE PROTOMERS WHERE THE 140 - 150 LOOP FROM D, J, RESPECTIVELY, CHELATES TO THE CALCIUM IONS) APPEARS TO ADOPT A DIFFERENT ROTAMER (CHI2+180) THAN THAT IN THE OTHER 6 CALCIUM BOUND PROTOMERS. THE SIDE CHAIN OF GLU 147 ALSO ADOPTS DIFFERENT, BUT CONSISTENT, CONFORMATIONS IN THE VARIOUS CALCIUM BOUND PROTOMERS DEPENDING ON CRYSTAL CONTACTS.
Nonpolymer detailsTHE SECOND CALCIUM ION (502) IN PROTOMERS A AND B HAS A VERY LOW OCCUPANCY AND DOES NOT REFINE WELL. ...THE SECOND CALCIUM ION (502) IN PROTOMERS A AND B HAS A VERY LOW OCCUPANCY AND DOES NOT REFINE WELL. THUS A 502 AND B 502 HAVE BEEN PLACED, FOLLOWING FULL STRUCTURAL REFINEMENT, ACCORDING TO THE ELECTRON DENSITY PRESENT IN 2FO-FC MAPS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 65 %
Crystal grow
*PLUS
Temperature: 40 ℃ / Method: gel
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris11
20.14 M11NaCl
32 mM11CaCl2
410 mMTris12
50.14 M12NaCl
610 mMTris13
70.14 M13NaCl
82 mM13CaCl2
928 mg/mlCRP13

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.901
DetectorType: FILM / Detector: FILM / Date: Mar 1, 1988
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 57243 / % possible obs: 74 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Rmerge(I) obs: 0.138
Reflection
*PLUS
Num. measured all: 108430

-
Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4data collection
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data reduction
X-PLOR3.1phasing
RefinementResolution: 3→12 Å / σ(F): 3
Details: RESIDUES 142 - 145 IN CHAINS D AND J ARE NOT TIED DOWN. LOOP 140-150 IN PROTOMER J (NO CALCIUM) IS LOOSELY ASSOCIATED WITH MAIN BODY OF PROTEIN. IT FORMS SYMMETRY CONTACT TO PROTOMER I WITH ...Details: RESIDUES 142 - 145 IN CHAINS D AND J ARE NOT TIED DOWN. LOOP 140-150 IN PROTOMER J (NO CALCIUM) IS LOOSELY ASSOCIATED WITH MAIN BODY OF PROTEIN. IT FORMS SYMMETRY CONTACT TO PROTOMER I WITH GLU 147 J CHELATING TO CALCIUM IONS IN PROTOMER I. LOOP 140-150 IN PROTOMER D (NO CALCIUM) IS LOOSELY ASSOCIATED WITH MAIN BODY OF PROTEIN. IT FORMS SYMMETRY CONTACT TO PROTOMER C WITH GLU 147 D CHELATING TO CALCIUM IONS IN PROTOMER C. THE UNCERTAINTY IN RESIDUES 142 - 145 IN CHAINS D AND J RESULTS IN 2.4 A CLOSE NON-BONDED CONTACTS D 142 - D 143 AND J 142 - J 143. RESIDUE LEU 43 IN CHAINS D AND J FALLS IN A GENEROUSLY ALLOWED POSITION ON THE RAMACHANDRAN PLOT. THIS MINOR UNCERTAINTY IN THIS REGION IN PROTOMERS D AND J RESULTS IN TWO 2.6 A NON-BONDED CONTACTS IN EACH PROTOMER (D 42 - D 43, D 44 - D 45 , J 42 - J 43, J 44 - J 45).
RfactorNum. reflection% reflection
Rfree0.273 -5 %
Rwork0.239 --
obs0.239 39996 74 %
Displacement parametersBiso mean: 25.8 Å2
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16320 0 16 0 16336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.587
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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