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- PDB-4ip8: Structure of human serum amyloid A1 -

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Basic information

Entry
Database: PDB / ID: 4ip8
TitleStructure of human serum amyloid A1
ComponentsSerum amyloid A-1 protein
KeywordsPROTEIN BINDING / secondary amyloid / four-helix bundle / main constituent of secondary amyloid / Toll like receptor / human serum
Function / homology
Function and homology information


Scavenging by Class B Receptors / lymphocyte chemotaxis / positive regulation of interleukin-1 production / high-density lipoprotein particle / Formyl peptide receptors bind formyl peptides and many other ligands / macrophage chemotaxis / regulation of protein secretion / cytoplasmic microtubule / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling ...Scavenging by Class B Receptors / lymphocyte chemotaxis / positive regulation of interleukin-1 production / high-density lipoprotein particle / Formyl peptide receptors bind formyl peptides and many other ligands / macrophage chemotaxis / regulation of protein secretion / cytoplasmic microtubule / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / endocytic vesicle lumen / neutrophil chemotaxis / positive regulation of cell adhesion / positive regulation of cytokine production / acute-phase response / G protein-coupled receptor binding / TAK1-dependent IKK and NF-kappa-B activation / platelet activation / negative regulation of inflammatory response / heparin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / Interleukin-4 and Interleukin-13 signaling / G alpha (q) signalling events / Amyloid fiber formation / extracellular exosome / extracellular region
Similarity search - Function
Serum amyloid A protein / Serum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins / Topoisomerase I; Chain A, domain 4 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / Serum amyloid A-1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.193 Å
AuthorsLu, J. / Sun, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural mechanism of serum amyloid A-mediated inflammatory amyloidosis.
Authors: Lu, J. / Yu, Y. / Zhu, I. / Cheng, Y. / Sun, P.D.
History
DepositionJan 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum amyloid A-1 protein
B: Serum amyloid A-1 protein
C: Serum amyloid A-1 protein
D: Serum amyloid A-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,27619
Polymers47,3244
Non-polymers3,95215
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-76 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.591, 128.419, 50.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-325-

HOH

21B-315-

HOH

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Components

#1: Protein
Serum amyloid A-1 protein / SAA / Amyloid protein A / Amyloid fibril protein AA / Serum amyloid protein A(2-104) / Serum ...SAA / Amyloid protein A / Amyloid fibril protein AA / Serum amyloid protein A(2-104) / Serum amyloid protein A(3-104) / Serum amyloid protein A(2-103) / Serum amyloid protein A(2-102) / Serum amyloid protein A(4-101)


Mass: 11830.892 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DJI8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C14H28O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0M (NH4)2SO4, 0.1M Hepes, 6% PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 23335 / Num. obs: 22939 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Biso Wilson estimate: 36.8 Å2 / Rsym value: 0.098 / Net I/σ(I): 24.4
Reflection shellResolution: 2.19→2.3 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 1413 / Rsym value: 0.489 / % possible all: 92.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.193→46.754 Å / SU ML: 0.69 / σ(F): 1.33 / Phase error: 32.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1183 5.17 %Random
Rwork0.2038 ---
obs0.2065 22904 97.62 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.6 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4086 Å2-0 Å20 Å2
2---11.7118 Å2-0 Å2
3---14.1204 Å2
Refinement stepCycle: LAST / Resolution: 2.193→46.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 110 101 3559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033543
X-RAY DIFFRACTIONf_angle_d0.6654728
X-RAY DIFFRACTIONf_dihedral_angle_d15.4421297
X-RAY DIFFRACTIONf_chiral_restr0.054400
X-RAY DIFFRACTIONf_plane_restr0.003644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1934-2.29320.33531280.26152597X-RAY DIFFRACTION94
2.2932-2.41410.31921280.23272658X-RAY DIFFRACTION98
2.4141-2.56540.31221590.20882670X-RAY DIFFRACTION98
2.5654-2.76340.33671330.22352709X-RAY DIFFRACTION98
2.7634-3.04150.27921570.21842692X-RAY DIFFRACTION98
3.0415-3.48140.27281570.21482735X-RAY DIFFRACTION99
3.4814-4.38570.23181570.17322766X-RAY DIFFRACTION99
4.3857-46.76450.19491640.19362894X-RAY DIFFRACTION98

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