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- PDB-2xrc: Human complement factor I -

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Basic information

Entry
Database: PDB / ID: 2xrc
TitleHuman complement factor I
ComponentsHUMAN COMPLEMENT FACTOR I
KeywordsIMMUNE SYSTEM / HYDROLASE / CONGLUTINOGEN ACTIVATING FACTOR / SERINE PROTEASE / COMPLEMENT SYSTEM
Function / homology
Function and homology information


complement factor I / complement activation, classical pathway / Regulation of Complement cascade / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding
Similarity search - Function
: / : / Complement factor I, FIMAC N-terminal domain / Complement factor I, KAZAL domain / Mac-2 Binding Protein / SRCR-like domain / Scavenger receptor cysteine-rich domain / Factor I / membrane attack complex / factor I membrane attack complex / SRCR domain ...: / : / Complement factor I, FIMAC N-terminal domain / Complement factor I, KAZAL domain / Mac-2 Binding Protein / SRCR-like domain / Scavenger receptor cysteine-rich domain / Factor I / membrane attack complex / factor I membrane attack complex / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsRoversi, P. / Johnson, S. / Lea, S.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural Basis for Complement Factor I Control and its Disease-Associated Sequence Polymorphisms.
Authors: Roversi, P. / Johnson, S. / Caesar, J.J. / Mclean, F. / Leath, K.J. / Tsiftsoglou, S.A. / Morgan, B.P. / Harris, C.L. / Sim, R.B. / Lea, S.M.
History
DepositionSep 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DJ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN COMPLEMENT FACTOR I
B: HUMAN COMPLEMENT FACTOR I
C: HUMAN COMPLEMENT FACTOR I
D: HUMAN COMPLEMENT FACTOR I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,33734
Polymers254,1494
Non-polymers5,18730
Water00
1
A: HUMAN COMPLEMENT FACTOR I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9459
Polymers63,5371
Non-polymers1,4078
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HUMAN COMPLEMENT FACTOR I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9459
Polymers63,5371
Non-polymers1,4078
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HUMAN COMPLEMENT FACTOR I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7248
Polymers63,5371
Non-polymers1,1867
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HUMAN COMPLEMENT FACTOR I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7248
Polymers63,5371
Non-polymers1,1867
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.317, 234.721, 40.300
Angle α, β, γ (deg.)89.98, 90.18, 90.03
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999323, 0.011615, -0.034902), (-0.011806, -0.999916, 0.00526), (-0.034838, 0.005669, 0.999377)104.7023, 211.2446, 6.7382
2given(0.999688, -0.009196, 0.023227), (-0.009214, -0.999957, 0.000657), (0.02322, -0.000871, -0.99973)-34.1096, 93.7187, -6.7457
3given(-0.999998, 0.000797, 0.002081), (0.000797, 1, -0.000346), (-0.002081, -0.000344, -0.999998)70.5601, -117.3152, 0.1191

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Components

#1: Protein
HUMAN COMPLEMENT FACTOR I / C3B/C4B INACTIVATOR / COMPLEMENT FACTOR I HEAVY CHAIN / COMPLEMENT FACTOR I LIGHT CHAIN / KAF


Mass: 63537.355 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: SERUM / References: UniProt: P05156, complement factor I
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Nonpolymer detailsN-ACETYLGLUCOSAMINE (NAG): N-LINKED GLYCOSYLATION
Sequence detailsTHE PROTEIN IN THIS ENTRY IS THE MATURE FORM OF FACTOR I. THEREFORE THE SIGNAL PEPTIDE (FIRST 18 ...THE PROTEIN IN THIS ENTRY IS THE MATURE FORM OF FACTOR I. THEREFORE THE SIGNAL PEPTIDE (FIRST 18 RESIDUES) OF THE UNIPROT ENTRY IS MISSING FROM THE SAMPLE, AND SO IS THE SEQUENCE RRKR AT RESIDUE NUMBERS 336-339.

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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: 2.65 Å3/Da / Density % sol: 54 %
Description: THE CRYSTAL AND DATA WERE TETARTOHEDRALLY TWINNED.
Crystal growpH: 4
Details: 20.0-23.5% PEG 1500, 0.1M SODIUM SUCCINATE PH 4.0, 1MM CACL2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 30, 2009 / Details: MIRRORS
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.334
11-H, K, -L20.359
11-h,-k,l30.187
11h,-k,-l40.119
ReflectionResolution: 2.65→79 Å / Num. obs: 68978 / % possible obs: 90.8 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.5
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0079refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1EKB, 1BY2, 1J8E AND 3B4V

1ekb

1by2

1j8e

3b4v


Resolution: 2.69→79 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.876 / SU B: 16.144 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED BUT NOT DEPOSITED. TETARTOHEDRAL TWINNING
RfactorNum. reflection% reflectionSelection details
Rfree0.23821 3252 5 %RANDOM
Rwork0.19959 ---
obs0.20151 61930 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.172 Å2
Baniso -1Baniso -2Baniso -3
1-40.54 Å2-11.14 Å25.73 Å2
2---24.97 Å2-8.07 Å2
3----15.57 Å2
Refinement stepCycle: LAST / Resolution: 2.69→79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14581 0 316 0 14897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215290
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210328
X-RAY DIFFRACTIONr_angle_refined_deg0.91.96120687
X-RAY DIFFRACTIONr_angle_other_deg0.765325170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51851827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75624.474675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.637152552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8481570
X-RAY DIFFRACTIONr_chiral_restr0.0540.22248
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216707
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023039
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.691→2.761 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 236 -
Rwork0.232 3877 -
obs--78.18 %

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