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- PDB-5jtw: Crystal structure of complement C4b re-refined using iMDFF -

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Basic information

Entry
Database: PDB / ID: 5jtw
TitleCrystal structure of complement C4b re-refined using iMDFF
Components(Complement C4-A) x 3
KeywordsIMMUNE SYSTEM / innate immune system / complement / active form
Function / homology
Function and homology information


complement component C1q complex binding / positive regulation of apoptotic cell clearance / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...complement component C1q complex binding / positive regulation of apoptotic cell clearance / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood microparticle / inflammatory response / endoplasmic reticulum lumen / axon / innate immune response / neuronal cell body / synapse / dendrite / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Complement C4, MG1 domain / Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / N-terminal domain of TfIIb / Alpha-2-macroglobulin, conserved site ...: / Complement C4, MG1 domain / Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / N-terminal domain of TfIIb / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Glycosyltransferase - #20 / : / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Other non-globular / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Single Sheet / Special / Jelly Rolls / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCroll, T.I. / Andersen, G.R.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Aarhus University Research Foundation Denmark
Danish Science Research Council for Nature and Universe Denmark
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.
Authors: Croll, T.I. / Andersen, G.R.
#1: Journal: J Immunol. / Year: 2015
Title: Structural Basis for the Function of Complement Component C4 within the Classical and Lectin Pathways of Complement.
Authors: Mortensen, S. / Kidmose, R.T. / Petersen, S.V. / Szilagyi, A. / Prohaszka, Z. / Andersen, G.R.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
SupersessionAug 10, 2016ID: 4xam
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Structure summary
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 28, 2016Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 7, 2024Group: 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: Complement C4-A
B: Complement C4-A
C: Complement C4-A
D: Complement C4-A
E: Complement C4-A
F: Complement C4-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,65710
Polymers360,7736
Non-polymers8854
Water00
1
A: Complement C4-A
B: Complement C4-A
C: Complement C4-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,8295
Polymers180,3863
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-83 kcal/mol
Surface area69380 Å2
MethodPISA
2
D: Complement C4-A
E: Complement C4-A
F: Complement C4-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,8295
Polymers180,3863
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17280 Å2
ΔGint-81 kcal/mol
Surface area68700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.500, 161.080, 131.600
Angle α, β, γ (deg.)90.000, 107.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Complement C4-A / Acidic complement C4 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 2


Mass: 71761.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C0L4
#2: Protein Complement C4-A / Acidic complement C4 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 2


Mass: 75508.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C0L4
#3: Protein Complement C4-A / Acidic complement C4 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 2


Mass: 33115.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C0L4
#4: 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.: 4
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

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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: 3.41 Å3/Da / Density % sol: 63.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: the crystals appeared after mixing C4b at 4 mg/ml in 20 mM HEPES pH 7.5, 100 mM sodium chloride with 100 mM HEPES pH 7.0, 400 mM magnesium chloride, 7.5% PEG8000 and a microseeding stock at ...Details: the crystals appeared after mixing C4b at 4 mg/ml in 20 mM HEPES pH 7.5, 100 mM sodium chloride with 100 mM HEPES pH 7.0, 400 mM magnesium chloride, 7.5% PEG8000 and a microseeding stock at the volume ration 1:1:0.5. The crystals appeared in 1-2 weeks and reached the final size in 1 month

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2014
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.5→49.54 Å / Num. obs: 60261 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 7.14 % / Biso Wilson estimate: 101.32 Å2 / CC1/2: 0.949 / Rmerge(I) obs: 0.492 / Net I/σ(I): 4.55
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.5-3.593.1330.65199.3
3.59-3.682.5910.8199.5
3.68-3.792.2690.89199.4
3.79-3.921.831.09198.9
3.92-4.061.3871.41198.2
4.06-4.211.0451.8198.6
4.21-4.40.7632.62199.4
4.4-4.640.5343.59199.2
4.64-4.930.4114.59198.6
4.93-5.310.3794.87198.2
5.31-5.850.3554.98198.6
5.85-6.690.3155.92198.6
6.69-8.420.1749.53197.6
8.420.07320.82196.1

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Processing

Software
NameVersionClassification
PHENIXdev_2376refinement
PDB_EXTRACT3.2data extraction
XDSNovember 11, 2013data reduction
XSCALEOct 15, 2015data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xam

4xam
PDB Unreleased entry


Resolution: 3.5→49.376 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.55
RfactorNum. reflection% reflection
Rfree0.2935 2014 3.34 %
Rwork0.248 --
obs0.2495 60234 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 289.39 Å2 / Biso mean: 122.3647 Å2 / Biso min: 33.53 Å2
Refinement stepCycle: final / Resolution: 3.5→49.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24256 0 56 0 24312
Biso mean--152.13 --
Num. residues----3128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324860
X-RAY DIFFRACTIONf_angle_d0.82633760
X-RAY DIFFRACTIONf_chiral_restr0.0473798
X-RAY DIFFRACTIONf_plane_restr0.0094390
X-RAY DIFFRACTIONf_dihedral_angle_d14.34714998
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.58750.3621430.34344202434599
3.5875-3.68450.39141480.33424135428399
3.6845-3.79290.33751430.333841844327100
3.7929-3.91520.37821330.32284179431299
3.9152-4.05510.40691480.31464129427798
4.0551-4.21740.35961500.28444090424099
4.2174-4.40920.32311330.26524207434099
4.4092-4.64150.29061500.23464155430599
4.6415-4.93210.21831380.21024146428499
4.9321-5.31250.31581450.22054161430698
5.3125-5.84630.2771470.23474136428399
5.8463-6.69050.30341400.24174201434199
6.6905-8.42260.29621490.22384134428398
8.4226-49.38050.19681470.18914161430897
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)
13.5629-0.03111.7834.3609-0.59566.31820.17720.26620.0979-0.1012-0.6194-1.20440.58671.05210.35720.81480.317-0.04921.01660.02471.03918.9984-6.9388-33.856
23.31451.74891.78418.1469-0.25773.36030.10350.5055-0.07570.32280.0837-1.2530.02410.78730.06850.43470.01420.09850.83640.00150.7313-9.338723.6542-48.2417
33.0166-0.3746-0.37526.16432.32751.9495-0.0950.1304-0.4138-0.7417-0.052-0.1964-0.03991.08130.09931.2630.0851-0.12611.17430.06950.7125-18.466219.2084-83.9103
42.04870.0791.28313.4184-1.49651.50070.45031.1999-0.6785-0.7122-0.4840.27120.45290.49750.19691.9540.5926-0.18041.5722-0.14530.9667-2.8543-13.0547-73.2289
54.38771.6084-1.18114.27260.61252.49030.13220.544-0.743-0.8882-0.27460.34850.8859-0.07710.07231.58620.2077-0.14211.0191-0.14660.9099-5.2245-17.0846-49.8852
60.31060.7555-0.46342.4378-0.05782.76970.04490.18830.1672-0.216-0.04860.4541-0.3816-0.3397-0.56760.0942-0.15270.24660.6001-0.0340.6598-34.900522.6295-52.7962
71.7406-1.23530.35713.2729-1.02630.3154-0.04980.8454-0.2444-1.0864-0.131-0.4310.04760.76530.29021.29270.19510.07981.2162-0.07820.8388-0.71150.9903-53.2876
83.01541.0184-0.78216.3254-0.63885.6790.16860.0560.16720.39850.20410.0263-0.163-0.299-0.23531.1301-0.0064-0.21960.54640.09750.728-38.032542.6379-68.3371
92.3237-2.57250.47512.9811-1.11863.3569-0.5533-0.45870.59030.38960.0905-0.7774-0.05050.76780.62081.4965-0.2631-0.10011.65530.26651.81634.609943.5832-51.7082
100.51290.1778-0.81782.6803-1.01081.62720.1049-0.00480.66090.3903-0.6675-1.7745-0.47551.58270.53861.47360.0237-0.34872.21450.23262.804940.36688.3854-32.7937
116.0493-1.5136-2.63186.32490.15563.95880.1164-0.0604-0.1601-0.501-0.00360.0692-0.28650.357-0.1611.00090.002-0.22390.628-0.04020.4743-29.704243.5841-88.1934
124.5264-4.6366-1.94238.67642.98772.34920.3241-0.70780.44360.3710.06970.19430.0976-0.1998-0.42391.77980.0843-0.02411.22470.00081.1042-41.285876.1477-60.2693
134.3160.13580.30634.70410.28083.297-0.2831-0.4510.32430.64120.2892-0.1112-0.9398-0.56260.08310.790.1649-0.0580.38-0.02590.5681-39.788112.0032-22.8169
144.0986-0.52480.82544.2181-0.89613.4302-0.2609-0.79770.40040.4980.0524-0.0769-0.85350.01570.41041.30910.1943-0.18120.913-0.05060.7629-15.3978-7.6438-0.5339
153.04910.39481.69621.17921.24822.43260.1158-0.3892-0.36040.1647-0.00250.41170.305-0.3128-0.04041.51190.1672-0.23461.0940.26661.0497-28.7636-42.3626.1465
166.29460.7512-0.40362.90311.86263.63770.4331-0.4165-0.19850.35050.01690.14030.4514-0.2771-0.24930.9053-0.183-0.09220.62150.16550.6322-52.4063-27.8153-18.3844
175.4278-2.09010.21696.41370.55144.73830.463-0.0295-0.344-0.8642-0.06590.32730.558-0.0201-0.48050.7609-0.0533-0.0150.5335-0.00640.5081-42.6461-10.0941-30.6996
182.3475-0.84581.13662.9052-1.48821.21320.17630.23970.05-0.325-0.1163-0.33730.59970.3972-0.02651.53440.2036-0.17181.033-0.02870.7585-1.1797-26.7792-10.1103
193.4468-1.32961.33491.585-1.21840.9698-0.461-1.0174-0.10871.32820.43630.06510.1937-0.29270.00061.2102-0.0065-0.18380.70850.04070.7851-36.972-8.8505-12.8333
204.41030.02260.28752.98680.45492.8120.14540.2428-0.06730.0937-0.380.13120.32880.3240.30341.53920.3263-0.44870.93810.07730.99025.0904-39.284611.5687
213.20771.53281.65732.19060.54560.8931-0.77160.56260.30850.53320.30580.1322-0.9714-0.04980.49392.06430.3214-0.291.9932-0.24441.2506-15.5126-0.232323.2213
223.5857-0.31521.2393.68511.26965.172-0.1961-1.19290.58920.19450.1223-0.1035-0.1442-0.56950.01640.9690.3917-0.0441.3708-0.3170.848-50.553934.2321.6694
236.28551.3499-0.31820.95370.00563.581-0.0277-0.6824-0.37930.01710.19580.42640.1938-0.6982-0.26011.73840.1223-0.37521.13150.17441.0436-9.6188-50.377823.3247
242.920.5713-1.34194.51050.90712.1559-0.30290.03770.2148-0.8820.1687-0.4161-0.31481.16390.02921.5469-0.0918-0.38441.68740.17191.161227.9982-33.675438.5109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1resid 20:139 and chain AA20 - 139
2X-RAY DIFFRACTION2(resid 140:236 or resid 1801) and chain AA140 - 236
3X-RAY DIFFRACTION2(resid 140:236 or resid 1801) and chain AA1801
4X-RAY DIFFRACTION3resid 237:361 and chain AA237 - 361
5X-RAY DIFFRACTION4resid 362:468 and chain AA362 - 468
6X-RAY DIFFRACTION5resid 469:568 and chain AA469 - 568
7X-RAY DIFFRACTION6(chain A and resid 569:605) or (chain B and resid 757:831)A569 - 605
8X-RAY DIFFRACTION6(chain A and resid 569:605) or (chain B and resid 757:831)B757 - 831
9X-RAY DIFFRACTION7resid 606:670 and chain AA606 - 670
10X-RAY DIFFRACTION8(resid 832:934 or resid 1802) and chain BB832 - 934
11X-RAY DIFFRACTION8(resid 832:934 or resid 1802) and chain BB1802
12X-RAY DIFFRACTION9(resid 935:982 or resid 1321:1392) and chain BB935 - 982
13X-RAY DIFFRACTION9(resid 935:982 or resid 1321:1392) and chain BB1321 - 1392
14X-RAY DIFFRACTION10resid 983:1320 and chain BB983 - 1320
15X-RAY DIFFRACTION11(chain B and resid 1393:1413) or (chain C and resid 1464:1579)B1393 - 1413
16X-RAY DIFFRACTION11(chain B and resid 1393:1413) or (chain C and resid 1464:1579)C1464 - 1579
17X-RAY DIFFRACTION12resid 1580:1744 and chain CC1580 - 1744
18X-RAY DIFFRACTION13resid 20:139 and chain DD20 - 139
19X-RAY DIFFRACTION14(resid 140:236 or resid 1801) and chain DD140 - 236
20X-RAY DIFFRACTION14(resid 140:236 or resid 1801) and chain DD1801
21X-RAY DIFFRACTION15resid 237:361 and chain DD237 - 361
22X-RAY DIFFRACTION16resid 362:468 and chain DD362 - 468
23X-RAY DIFFRACTION17resid 469:568 and chain DD469 - 568
24X-RAY DIFFRACTION18(chain D and resid 569:605) or (chain E and resid 757:831)D569 - 605
25X-RAY DIFFRACTION18(chain D and resid 569:605) or (chain E and resid 757:831)E757 - 831
26X-RAY DIFFRACTION19resid 606:670 and chain DD606 - 670
27X-RAY DIFFRACTION20(resid 832:934 or resid 1802) and chain EE832 - 934
28X-RAY DIFFRACTION20(resid 832:934 or resid 1802) and chain EE1802
29X-RAY DIFFRACTION21(resid 935:982 or resid 1321:1392) and chain EE935 - 982
30X-RAY DIFFRACTION21(resid 935:982 or resid 1321:1392) and chain EE1321 - 1392
31X-RAY DIFFRACTION22resid 983:1320 and chain EE983 - 1320
32X-RAY DIFFRACTION23(chain E and resid 1393:1413) or (chain F and resid 1464:1579)E1393 - 1413
33X-RAY DIFFRACTION23(chain E and resid 1393:1413) or (chain F and resid 1464:1579)F1464 - 1579
34X-RAY DIFFRACTION24resid 1580:1750 and chain FF1580 - 1750

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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