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- PDB-3zd2: THE STRUCTURE OF THE TWO N-TERMINAL DOMAINS OF COMPLEMENT FACTOR ... -

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Basic information

Entry
Database: PDB / ID: 3zd2
TitleTHE STRUCTURE OF THE TWO N-TERMINAL DOMAINS OF COMPLEMENT FACTOR H RELATED PROTEIN 1 SHOWS FORMATION OF A NOVEL DIMERISATION INTERFACE
ComponentsCOMPLEMENT FACTOR H-RELATED PROTEIN 1
KeywordsIMMUNE SYSTEM / CFHR-1 / CFHR1 / FHR1
Function / homology
Function and homology information


complement component C3b binding / complement activation / cytolysis by host of symbiont cells / negative regulation of protein binding / Regulation of Complement cascade / blood microparticle / protein-containing complex / extracellular space / extracellular region / identical protein binding
Similarity search - Function
: / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Complement factor H-related protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsCaesar, J.J.E. / Goicoechea de Jorge, E. / Pickering, M.C. / Lea, S.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Dimerization of Complement Factor H-Related Proteins Modulates Complement Activation in Vivo.
Authors: Goicoechea De Jorge, E. / Caesar, J.J.E. / Malik, T.H. / Patel, M. / Colledge, M. / Johnson, S. / Hakobyan, S. / Morgan, B.P. / Harris, C.L. / Pickering, M.C. / Lea, S.M.
History
DepositionNov 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMPLEMENT FACTOR H-RELATED PROTEIN 1
B: COMPLEMENT FACTOR H-RELATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,79118
Polymers28,7982
Non-polymers99316
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-15.6 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.270, 46.880, 111.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.916893, 0.371175, -0.146752), (0.361107, 0.614807, -0.701152), (-0.170026, -0.695874, -0.697746)
Vector: 25.117, 44.167, 114.968)

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Components

#1: Protein COMPLEMENT FACTOR H-RELATED PROTEIN 1 / FHR-1 / H FACTOR-LIKE PROTEIN 1 / H-FACTOR-LIKE 1 / H36


Mass: 14398.975 Da / Num. of mol.: 2 / Fragment: SCR DOMAINS 1 AND 2, RESIDUES 19-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KLUYVEROMYCES LACTIS (yeast) / Strain (production host): GG799 / References: UniProt: Q03591
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.3 % / Description: NONE
Crystal growpH: 6.5 / Details: 36% (W/V) PEG 2000 MME, 0.1M MES PH 6.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.7105
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2011 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7105 Å / Relative weight: 1
ReflectionResolution: 1.99→55.83 Å / Num. obs: 16303 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 34.82 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.2
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.9 / % possible all: 90.6

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UWN

2uwn


Resolution: 1.99→55.83 Å / Cor.coef. Fo:Fc: 0.9153 / Cor.coef. Fo:Fc free: 0.9156 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.245 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.18
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 818 5.03 %RANDOM
Rwork0.2211 ---
obs0.2224 16261 95.95 %-
Displacement parametersBiso mean: 51.16 Å2
Baniso -1Baniso -2Baniso -3
1--11.6963 Å20 Å20 Å2
2---1.4911 Å20 Å2
3---13.1874 Å2
Refine analyzeLuzzati coordinate error obs: 0.313 Å
Refinement stepCycle: LAST / Resolution: 1.99→55.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 64 102 2119
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082070HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.972788HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d670SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes290HARMONIC5
X-RAY DIFFRACTIONt_it2070HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion18.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion261SEMIHARMONIC5
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_contact2347SEMIHARMONIC4
LS refinement shellResolution: 1.99→2.13 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2539 126 4.63 %
Rwork0.2174 2598 -
all0.219 2724 -
obs--95.95 %
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)
11.14260.60142.69871.22910.73614.82910.0487-0.0875-0.07590.0815-0.0248-0.23740.23260.1761-0.0240.0042-0.03780.0112-0.0534-0.0189-0.088228.246740.925645.7816
22.1672-0.01240.0662.53831.61533.93280.0084-0.13120.03610.11820.03450.1221-0.0274-0.5442-0.0429-0.18390.03540.0373-0.0077-0.0026-0.19748.16147.682249.4842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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