7UE9: Anti-C3d Fab(3d8b)

Structure of anti-C3d Fab(3d8b) in complex with C3d. Determined by X-ray diffraction at 1.75 Å resolution. Released 8 Jun 2022.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 6,378
Mol. weight: 111.92 kDa
Released: 8 Jun 2022

Explore 7UE9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UE9 contains 39 α-helices and 55 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain C: 20 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
α-helix	4-10	7
α-helix	20-37	18
α-helix	41-44	4
α-helix	47-64	18
β-strand	67	1	14
β-strand	73	1	14
α-helix	80-82	3
α-helix	83-95	13
α-helix	96-98	3
α-helix	104-118	15
β-strand	119	1	15
β-strand	125	1	15
α-helix	134-141	8
α-helix	146-165	20
α-helix	166-168	3
α-helix	172-186	15
α-helix	187-189	3
α-helix	193-204	12
α-helix	211-220	10
β-strand	222	1	16
β-strand	226	1	16
α-helix	233-250	18
α-helix	253-255	3
α-helix	256-265	10
α-helix	276-292	17

Chain H: 11 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	58-60	3	8
α-helix	62-64	3
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-97	6	8
β-strand	101	1	8
β-strand	105-109	5	8
α-helix	112-114	3
β-strand	115	1	9
α-helix	116-117	2
β-strand	118-122	5	10
β-strand	126	1	11
β-strand	133-143	11	10
β-strand	144	1	9
β-strand	149-152	4	12
α-helix	153-155	3
β-strand	157	1	12
β-strand	161-163	3	10
α-helix	164-166	3
β-strand	167-168	2	10
β-strand	174-183	10	10
α-helix	184-186	3
β-strand	187	1	13
β-strand	190	1	13
β-strand	193-198	6	12
α-helix	199-201	3
β-strand	203-208	6	12
β-strand	213	1	11

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	30	1	3
β-strand	36	1	3
β-strand	38-43	6	2
β-strand	50-54	5	2
β-strand	58-59	2	2
α-helix	60	1
β-strand	67-72	6	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	89-95	7	2
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	116	1	4
α-helix	117-118	2
β-strand	119-123	5	5
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	5
β-strand	145	1	4
β-strand	150-155	6	6
β-strand	158-159	2	6
α-helix	160	1
β-strand	164-168	5	5
α-helix	169-172	4
β-strand	178-187	10	5
α-helix	188-192	5
β-strand	196-202	7	6
β-strand	210-215	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab light chain	L	protein	241	Mus musculus
Fab heavy chain	H	protein	456	Mus musculus
Complement C3dg fragment	C	protein	311	Homo sapiens	P01024 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>7UE9_1 Fab light chain (chains L)
MDMRVPAQLLGLLLLWLRGARCDVVMTQSPLSLPVTLGQPASISCKSSQSLLDSDGKTYL
NWFQQRPGQSPRRLIYLVSKLDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCWQGTH
FPRTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNA
LQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE
C

Sequence of entity 2 (H), FASTA

>7UE9_2 Fab heavy chain (chains H)
MGSTAILGLLLAVLQGVCAQVQLVQSGAEVKKPGASVKVSCKASGYTFTNYYINWVRQAP
GQGLEWMGVINPYSGGTSYNQKFKGRVTMTVDTSTSTAYMELSSLRSEDTAVYFCSSPYW
GQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPPCPPCP
APEFEGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTK
PREEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYT
LPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSRL
TVDKSRWQEGNVFSCSVLHEALHSHYTQKSLSLSLG

Sequence of entity 3 (C), FASTA

>7UE9_3 Complement C3dg fragment (chains C)
GAVDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKG
YTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQ
KPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKA
GDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEA
TSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPDHQEL
NLDVSLQLPSR

Primary citation

Development and Optimization of Bifunctional Fusion Proteins to Locally Modulate Complement Activation in Diseased Tissue. Fahnoe, K.C., Liu, F., Morgan, J.G. et al. Front Immunol (2022) 13:869725-869725. DOI 10.3389/fimmu.2022.869725 · PubMed

Other PDB entries of the same protein (UniProt P01024 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WY7 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
2WY8 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
1C3D 1.8 Å, X-ray crystal structure of C3D: a C3 fragment and ligand for complement receptor 2
6RMT 2.0 Å, Crystal structure of disulphide-linked human C3d dimer
7BAG 2.0 Å, C3b in complex with CP40
1GHQ 2.04 Å, CR2-C3D complex structure
3D5R 2.1 Å, Crystal Structure of Efb-C (N138A) / C3d Complex
3OXU 2.1 Å, Complement components factor H CCP19-20 and C3d in complex
4I6O 2.14 Å, Crystal structure of chemically synthesized human anaphylatoxin C3a
4ONT 2.15 Å, Ternary host recognition complex of complement factor H, C3d, and sialic acid
2GOX 2.2 Å, Crystal structure of Efb-C / C3d Complex
4ZH1 2.24 Å, Complement factor H in complex with the GM1 glycan

Browse structure collections

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