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- PDB-4ip9: Structure of native human serum amyloid A1 -

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Basic information

Entry
Database: PDB / ID: 4ip9
TitleStructure of native human serum amyloid A1
ComponentsSerum amyloid A-1 protein
KeywordsPROTEIN BINDING / double layer hexameric structure / secondary amyloid / High density lipoprotein / 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 / positive regulation of cell adhesion / endocytic vesicle lumen / neutrophil chemotaxis / 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 / G alpha (q) signalling events / Interleukin-4 and Interleukin-13 signaling / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2668
Polymers25,3202
Non-polymers1,9466
Water1086
1
A: Serum amyloid A-1 protein
B: Serum amyloid A-1 protein
hetero molecules

A: Serum amyloid A-1 protein
B: Serum amyloid A-1 protein
hetero molecules

A: Serum amyloid A-1 protein
B: Serum amyloid A-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,79724
Polymers75,9596
Non-polymers5,83918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8340 Å2
ΔGint-57 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.850, 93.850, 130.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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: 12659.771 Da / Num. of mol.: 2
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-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG2000 MME, 0.1M Tris (pH8.5) and 0.2 M Trimethylamine N-oxide, 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 / Date: Jul 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 7804 / Num. obs: 7791 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 71.11 Å2 / Rsym value: 0.102 / Net I/σ(I): 16.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3 / Num. unique all: 376 / Rsym value: 0.511 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→18.46 Å / Cor.coef. Fo:Fc: 0.9323 / Cor.coef. Fo:Fc free: 0.9244 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 752 9.68 %RANDOM
Rwork0.2491 ---
obs0.25 7768 --
Displacement parametersBiso mean: 82.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.7458 Å20 Å20 Å2
2--0.7458 Å20 Å2
3----1.4915 Å2
Refine analyzeLuzzati coordinate error obs: 0.595 Å
Refinement stepCycle: LAST / Resolution: 2.5→18.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 80 6 1744
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081782HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.862366HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d638SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes264HARMONIC5
X-RAY DIFFRACTIONt_it1782HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion19.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion190SEMIHARMONIC5
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_contact1974SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.79 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3079 206 9.41 %
Rwork0.2597 1984 -
all0.2641 2190 -
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)
17.5296-0.6011.29794.0044-0.93645.68890.5102-0.8481-1.18960.249-0.0541-0.03130.7172-0.3381-0.4561-0.0356-0.213-0.183-0.2420.2453-0.0094-5.5135-16.256743.3841
24.932-0.10081.78984.72810.63685.01210.56130.7741-0.3763-0.3764-0.33710.6718-0.0931-0.4843-0.2242-0.09130.0528-0.2246-0.101-0.1064-0.0928-10.9944-13.075517.6809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|104 }A1 - 104
2X-RAY DIFFRACTION2{ B|1 - B|104 }B1 - 104

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