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- PDB-4aqb: MBL-Ficolin Associated Protein-1, MAP-1 aka MAP44 -

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Basic information

Entry
Database: PDB / ID: 4aqb
TitleMBL-Ficolin Associated Protein-1, MAP-1 aka MAP44
ComponentsMANNAN-BINDING LECTIN SERINE PROTEASE 1
KeywordsBLOOD CLOTTING / MANNAN-BINDING PROTEIN / COMPLEMENT / FICOLINS / LECTIN COMPLEMENT PATHWAY / MANNOSE- BINDING LECTIN / MBL/FICOLIN ASSOCIATED PROTEIN-1 / MBL/FICOLIN ASSOCIATED SERINE PROTEASES / MAP1 / MAP44
Function / homology
Function and homology information


Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / negative regulation of complement activation / complement activation, lectin pathway / zymogen activation / Scavenging by Class A Receptors / Initial triggering of complement / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity ...Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / negative regulation of complement activation / complement activation, lectin pathway / zymogen activation / Scavenging by Class A Receptors / Initial triggering of complement / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / extracellular space / extracellular region / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / 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. ...Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / 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 / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / EGF-like domain signature 2. / EGF-like domain / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Mannan-binding lectin serine protease 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsSkjoedt, M.O. / Roversi, P. / Hummelshoj, T. / Palarasah, Y. / Johnson, S. / Lea, S.M. / Garred, P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure and Functional Characterization of the Complement Regulator Mannose-Binding Lectin (Mbl)/Ficolin-Associated Protein-1 (Map-1).
Authors: Skjoedt, M.O. / Roversi, P. / Hummelshoj, T. / Palarasah, Y. / Rosbjerg, A. / Johnson, S. / Lea, S.M. / Garred, P.
History
DepositionApr 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANNAN-BINDING LECTIN SERINE PROTEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3619
Polymers41,4611
Non-polymers1,9008
Water905
1
A: MANNAN-BINDING LECTIN SERINE PROTEASE 1
hetero molecules

A: MANNAN-BINDING LECTIN SERINE PROTEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,72218
Polymers82,9222
Non-polymers3,80016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area5620 Å2
ΔGint-43.4 kcal/mol
Surface area40610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.150, 94.150, 242.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein MANNAN-BINDING LECTIN SERINE PROTEASE 1 / MBL-FICOLIN ASSOCIATED PROTEIN-1 / COMPLEMENT FACTOR MASP-3 / COMPLEMENT-ACTIVATING COMPONENT OF RA- ...MBL-FICOLIN ASSOCIATED PROTEIN-1 / COMPLEMENT FACTOR MASP-3 / COMPLEMENT-ACTIVATING COMPONENT OF RA-REACTIVE FACTOR / MANNOSE-BINDING LECTIN-ASSOCIATED SERINE PROTEASE 1 / MASP-1 / MANNOSE-BINDING PROTEIN-ASSOCIATED SERINE PROTEASE / RA-REACTIVE FACTOR SERINE PROTEASE P100 / RARF / SERINE PROTEASE 5 / MANNAN-BINDING LECTIN SERINE PROTEASE 1 HEAVY CHAIN


Mass: 41460.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLASMA / Cell line (production host): CHO DG44 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P48740
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNO SIGNAL PEPTIDE RESIDUES 1-19 ISOFORM 3 OF MASP-1, AKA MAP-1, AKA MAP44

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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: 6.51 Å3/Da / Density % sol: 81.1 %
Description: DATA ANISOTROPICALLY TRUNCATED AND B-SHARPENED WITH A B=-5.85 AT THE UCLA SERVER HTTP SERVICES.MBI.UCLA.EDU ANISOSCALE ANISOSCALE_XDS
Crystal growpH: 6.5
Details: 0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 40% W/V PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.2→58.4 Å / Num. obs: 7844 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 3.64 % / Biso Wilson estimate: 129.96 Å2 / Rmerge(I) obs: 0.28 / Net I/σ(I): 8.7
Reflection shellResolution: 4.2→4.36 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.8 / % possible all: 95.2

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3DEM AND 3GOV

3dem

3gov


Resolution: 4.2→58.36 Å / Cor.coef. Fo:Fc: 0.8191 / Cor.coef. Fo:Fc free: 0.8216 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.797
Details: TLS REFINEMENT AND SECONDARY INITIAL COORDINATES FROM MOLECULAR REPLACEMENT. SECONDARY STRUCTURE RESTRAINTS TO THE INITIAL COORDINATES FROM MOLECULAR REPLACEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.3006 360 4.59 %RANDOM
Rwork0.2786 ---
obs0.2797 7843 91.8 %-
Displacement parametersBiso mean: 145.51 Å2
Baniso -1Baniso -2Baniso -3
1-8.7443 Å20 Å20 Å2
2--8.7443 Å20 Å2
3----17.4885 Å2
Refine analyzeLuzzati coordinate error obs: 1.502 Å
Refinement stepCycle: LAST / Resolution: 4.2→58.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 117 5 2896
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0062999HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.024073HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1049SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes422HARMONIC5
X-RAY DIFFRACTIONt_it2999HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion17.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion410SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance23HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3182SEMIHARMONIC4
LS refinement shellResolution: 4.2→4.7 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2617 89 4.46 %
Rwork0.2675 1908 -
all0.2672 1997 -
obs--91.8 %
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)
15.6274-1.4636-2.00466.92681.56887.72960.0749-0.535-0.056-0.3367-0.31830.5442-0.0866-0.5320.2435-0.2853-0.1520.03750.2851-0.152-0.2055-22.19811.84959.9228
22.63140.05482.91040-1.3433.2180.05870.19710.37890.5442-0.0249-0.295-0.2757-0.109-0.0338-0.0444-0.0984-0.06040.3040.1520.060514.61161.010511.899
38.31540.95541.56386.1439-2.90652.17750.00520.04430.5442-0.0050.0005-0.0840.15-0.1388-0.00570.2393-0.152-0.152-0.02460.0961-0.265338.38165.309928.6848
43.68720.9471.40683.4684-0.47270.55-0.03540.0541-0.1982-0.3990.18170.22310.11-0.0433-0.14630.2897-0.1488-0.1520.246-0.1476-0.303978.838210.507130.5146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 22-138, 702 AND 649-653)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 139-183, 678-681, 701)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 184-298, 703)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 299-366)

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