PDB-9d41: Crystal structure of N-terminal domain of Borealin (20-88) in com...

ID or keywords:

Entry

Database: PDB / ID: 9d41

Title

Crystal structure of N-terminal domain of Borealin (20-88) in complex with synthetic antibody fragment

Components

Borealin
Fab Heavy Chain
Fab Light Chain

Keywords

IMMUNE SYSTEM / Borealin / CPC core / Fab

Function / homology

Function and homology information

positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / chromosome passenger complex / mitotic metaphase chromosome alignment / spindle midzone / mitotic cytokinesis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.84 Å

Authors

Filippova, E.V. / Hou, J. / Mukherjee, S. / Kossiakoff, A.A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of N-terminal domain of Borealin (20-88) in complex with synthetic antibody fragment
Authors: Filippova, E.V. / Hou, J. / Mukherjee, S. / Kossiakoff, A.A.

History

Deposition	Aug 12, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 20, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9d41.cif.gz	220.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9d41.ent.gz	174.3 KB	Display	PDB format
PDBx/mmJSON format	9d41.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9d41_validation.pdf.gz	458.5 KB	Display	wwPDB validaton report
Full document	9d41_full_validation.pdf.gz	463.3 KB	Display
Data in XML	9d41_validation.xml.gz	28.5 KB	Display
Data in CIF	9d41_validation.cif.gz	39.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d4/9d41 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/9d41	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (6) #150 - Jun 2012 Sliding Clamps similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #245 - May 2020 Spliceosomes similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#205 - Jan 2017
Nuclear Pore Complex
similarity (6)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)

Deposited unit

A: Borealin

H: Fab Heavy Chain

L: Fab Light Chain

hetero molecules

57.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	72.432, 72.432, 243.129
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

-
Protein , 1 types, 1 molecules A

#1: Protein	Borealin / Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell- ...Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell-related gene 3 protein Mass: 8149.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA8, PESCRG3 / Plasmid: pHFT2 / Details (production host): PET based / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53HL2

#1: Protein

Borealin / Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell- ...

Mass: 8149.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: CDCA8, PESCRG3 / Plasmid: pHFT2 / Details (production host): PET based / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53HL2

-
Antibody , 2 types, 2 molecules HL

#2: Antibody	Fab Heavy Chain Mass: 25161.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: engineered Elbow region FNQIKG / Source: (gene. exp.) Homo sapiens (human) / Plasmid: RH2.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(gold)
#3: Antibody	Fab Light Chain Mass: 23283.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: engineered Crystal Kappa region / Source: (gene. exp.) Homo sapiens (human) / Plasmid: RH2.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(gold)

-
Non-polymers , 3 types, 374 molecules

#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.42 Å³/Da / Density % sol: 64.07 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 10.5 / Details: 0.1 M CAPS, 40 % v/v MPD

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 26, 2024 / Details: mirrors
Radiation	Monochromator: a double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.920105 Å / Relative weight: 1
Reflection	Resolution: 1.84→34.06 Å / Num. obs: 65038 / % possible obs: 100 % / Redundancy: 11.9 % / CC_1/2: 0.999 / R_pim(I) all: 0.059 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.84→1.87 Å / Num. unique obs: 3190 / CC_1/2: 0.353 / R_pim(I) all: 1.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.84→34.06 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.968 / SU B: 6.963 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19732	3300	5.1 %	RANDOM
R_work	0.15536	-	-	-
obs	0.15748	61029	98.82 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 46.586 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	-0.01 Å²	-0 Å²
2-	-	-0.02 Å²	0 Å²
3-	-	-	0.06 Å²

Refinement step

Cycle: 1 / Resolution: 1.84→34.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3803	0	81	363	4247

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	4013
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3658
X-RAY DIFFRACTION	r_angle_refined_deg	1.625	1.65	5472
X-RAY DIFFRACTION	r_angle_other_deg	1.448	1.573	8497
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.507	5	498
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.118	22.849	179
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.41	15	639
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.315	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	524
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4430
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	833
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	4.693	4.11	1986
X-RAY DIFFRACTION	r_mcbond_other	4.717		1985
X-RAY DIFFRACTION	r_mcangle_it	5.522	6.139	2486
X-RAY DIFFRACTION	r_mcangle_other	5.521	9.233	2487
X-RAY DIFFRACTION	r_scbond_it	7.162	4.905	2027
X-RAY DIFFRACTION	r_scbond_other	7.16	4.908	2028
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.785	7.074	2987
X-RAY DIFFRACTION	r_long_range_B_refined	7.794		4410
X-RAY DIFFRACTION	r_long_range_B_other	7.76		4325
X-RAY DIFFRACTION	r_rigid_bond_restr	5.013	3	3943
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.843→1.891 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.315	216	-
R_work	0.342	3818	-
obs	-	-	85.5 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.2759	0.1198	-0.1325	0.161	-0.0342	0.1664	-0.0164	-0.056	-0.0989	-0.0156	0.0069	-0.0509	0.0378	0.0138	0.0094	0.0244	0.0046	-0.0063	0.0546	0.0189	0.0506	-17.664	11.181	36.657
2	0.8896	0.6124	-0.6825	1.5704	-0.2425	1.3062	-0.0172	0.0352	0.0362	-0.0519	0.0361	0.0613	-0.0631	-0.0605	-0.0189	0.0357	0.0006	-0.0036	0.0468	-0.0013	0.0029	-22.077	24.74	33.115
3	0.551	0.1221	-0.0732	0.0884	-0.0177	0.0166	0.0117	-0.0571	-0.0217	0.0308	-0.0121	-0.0095	0.0102	0.0025	0.0004	0.0389	-0.0007	-0.0056	0.0521	0.0019	0.0058	-20.802	17.898	40.51
4	0.874	0.8549	0.7645	0.8981	0.79	0.7002	-0.0542	0.0606	-0.0988	-0.0027	0.0785	-0.0278	-0.0145	0.0433	-0.0243	0.0932	-0.0128	0.068	0.0895	-0.0122	0.0956	-24.098	14.88	26.934
5	0.21	-0.0469	-0.0576	0.1072	0.2265	0.6214	-0.0356	0.03	-0.0155	0.0095	-0.0031	0.0121	0.0977	-0.0657	0.0387	0.0704	-0.0318	0.0131	0.0486	-0.0041	0.0082	-27.126	15.153	3.917
6	0.4873	-0.1863	-0.2992	0.1132	0.103	0.474	0.0099	-0.0028	0.0092	0.0078	-0.006	0.0044	0.0031	-0.0014	-0.004	0.044	-0.0083	-0.0025	0.0328	-0.0001	0.0024	-20.472	14.441	5.309
7	0.4683	0.1656	-0.2542	0.4396	-0.1081	0.6369	0.0412	0.087	-0.0226	-0.0473	0.0208	0.0151	0.0395	-0.0236	-0.062	0.0515	-0.0092	-0.0053	0.0488	-0.0052	0.021	-18.321	10.971	-6.251
8	4.3453	1.4549	-2.786	0.4907	-0.8345	5.7294	0.1118	0.0451	0.3263	0.0305	0.0078	0.1148	-0.1323	-0.255	-0.1196	0.0289	0.0113	-0.0106	0.0609	0.0014	0.04	-17.788	39.86	38.359
9	0.2225	0.1159	0.1003	0.1292	-0.0172	0.487	-0.0113	-0.0299	0.0168	0.0019	0.0102	-0.0133	0.042	0.0131	0.0011	0.0362	-0.0011	-0.0055	0.0453	-0.0064	0.0157	-6.292	33.169	35.17
10	0.2071	0.0617	0.0063	0.0533	0.0854	0.6672	-0.0199	-0.0001	0.0052	0.0124	-0.0163	-0.0019	0.0207	0.0176	0.0362	0.0379	-0.0045	-0.0042	0.0559	0.0073	0.0046	-1.468	37.654	35.086
11	0.1246	0.0399	0.0272	0.0834	0.1391	0.2474	-0.0127	-0.0266	0.003	-0.0169	0.0063	0.0046	-0.0265	0.0173	0.0064	0.0322	-0.0033	-0.0045	0.0348	0.0024	0.0093	-11.985	29.999	27.941
12	0.056	0.1576	0.012	0.5246	-0.0471	0.116	0.0021	-0.0129	0.0224	0.0347	-0.0305	0.0453	0.0111	-0.0116	0.0284	0.0494	-0.0025	0.0031	0.0497	-0.0053	0.0143	-24.516	27.168	3.753
13	2.3812	1.543	1.8711	2.065	1.0812	1.6662	-0.0496	0.0399	-0.0385	-0.0378	0.0334	0.0146	-0.1147	0.0177	0.0162	0.0504	-0.0084	-0.0077	0.0463	-0.0059	0.0256	-21.393	35.134	0.548

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	L	1 - 34
2	X-RAY DIFFRACTION	2	L	35 - 46
3	X-RAY DIFFRACTION	3	L	47 - 100
4	X-RAY DIFFRACTION	4	L	101 - 107
5	X-RAY DIFFRACTION	5	L	108 - 125
6	X-RAY DIFFRACTION	6	L	126 - 181
7	X-RAY DIFFRACTION	7	L	182 - 213
8	X-RAY DIFFRACTION	8	H	4 - 10
9	X-RAY DIFFRACTION	9	H	11 - 67
10	X-RAY DIFFRACTION	10	H	68 - 89
11	X-RAY DIFFRACTION	11	H	90 - 138
12	X-RAY DIFFRACTION	12	H	139 - 210
13	X-RAY DIFFRACTION	13	H	211 - 215

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules A

-
Antibody , 2 types, 2 molecules HL

-
Non-polymers , 3 types, 374 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 1 molecules A

-Antibody , 2 types, 2 molecules HL

-Non-polymers , 3 types, 374 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules A

-
Antibody , 2 types, 2 molecules HL

-
Non-polymers , 3 types, 374 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi